Library preparation systems and related methods

Abstract

A library preparation system and method are disclosed. In one implementation, a modular bay for preparing a library of samples for sequencing includes a contact dispenser and a work area, the work area including a work plate receptacle adapted to receive a work plate, a thermocycler, a magnet, and a drawer. The drawer includes a consumable area adapted to receive a sample plate adapted to contain a sample, and a plurality of consumables for interacting with the sample in the work plate. The contact dispenser is linearly movable longitudinally between the consumable area and the work area, and is configured to (i) transfer a sample from a sample plate in the consumable area to a work plate in the work area, and (ii) transfer a plurality of consumables between the consumable area and the work plate in the work area.

Description

[Technical Field]

[0001] Related Applications This application claims the benefit of and priority to U.S. Provisional Patent Application No. 63 / 433,389, filed December 16, 2022, the contents of which are incorporated herein by reference in their entirety for all purposes. [Background technology]

[0002] A DNA library can be prepared to allow the sample to be sequenced. Summary of the Invention

[0003] Through the provision of library preparation systems and methods, deficiencies in the prior art can be overcome and advantages can be realized as described below in this disclosure. Various implementations of the devices and methods are described below, and the devices and methods, including and excluding the additional implementations listed below, in any combination (provided that such combinations are not inconsistent), can overcome these deficiencies and achieve the benefits described herein.

[0004] In a first implementation, a modular system for preparing a library of samples for sequencing is disclosed, the modular system including a first assay bay, a common bay, and a mover. The first assay bay includes a first contact dispenser, a first work area, and a first drawer. The first work area includes a work plate receptacle adapted to receive a work plate, a thermocycler, and a magnet. The first drawer includes a consumable area adapted to receive a sample plate adapted to contain samples and a plurality of consumables for interacting with the samples in the work plate. The common bay includes an analyzer area including an imaging system. The mover is operably coupled to the first assay bay and the common bay. The first contact dispenser is linearly movable in a first direction between the consumable area and the first work area, and is configured to (i) move a sample from a sample plate in the consumable area to a work plate in the first work area and (ii) move a plurality of consumables between the consumable area and the work plate in the first work area. The mover is movable in the first direction and a second direction perpendicular to the first direction between the first assay bay and the common bay, and is configured to move the work plate from the first work area to the analyzer area for analysis by the imaging system.

[0005] In a second implementation, a modular bay for preparing a library of samples for sequencing is disclosed, the modular bay including a contact dispenser, a work area including a work plate receptacle adapted to receive a work plate, a thermocycler, a magnet, and a drawer. The drawer includes a consumable area adapted to receive a sample plate adapted to contain a sample, and a plurality of consumables for interacting with the sample in the work plate. The contact dispenser is linearly movable longitudinally between the consumable area and the work area, and is configured to (i) transfer a sample from the sample plate in the consumable area to the work plate in the work area and (ii) transfer the plurality of consumables between the consumable area and the work plate in the work area.

[0006] In a third implementation, the apparatus includes a system having a consumable area including a consumable receptacle, a mover, a contact dispenser, a stage for moving the contact dispenser, a plate receptacle, a magnet, a thermocycler, and an analyzer area including an imaging system. The consumable receptacle receives a chip tray including first and second chips, a first plate having wells for containing samples, a second plate having wells, an index tray having wells for containing indexes, and a bead tray having wells for containing beads.

[0007] In a fourth implementation, an apparatus is provided that includes a library preparation system and a sequencing system fluidly coupled to the library preparation system. In a fifth implementation, an apparatus is provided that includes a system including a bay, a second work area, a second contact dispenser, a second stage, and a mover. The bay includes a consumable area and a work area. The consumable area includes a consumable receptacle, a first contact dispenser, and a stage for moving the first contact dispenser. The work area includes a first plate receptacle, a magnet, and a thermocycler. The second work area includes a second plate receptacle, and the analyzer area includes an imaging system. The second stage moves the second contact dispenser relative to the first bay and the second work area.

[0008] In a sixth implementation, an apparatus is provided that includes a system having a consumable area, a mover, a work area, a magnet, a thermocycler, an analyzer area, and a reagent reservoir receptacle for receiving a reagent reservoir. The consumable area includes a chip tray including a first chip and a second chip, a first plate having wells for containing samples, a second plate having wells, an index tray having wells for containing indexes, and a bead tray having wells for containing beads. The work area includes a contact dispenser, a non-contact dispenser, and a stage including a first plate receptacle, a second plate receptacle, and a third plate receptacle. The analyzer area includes a substrate and an imaging system. The mover moves the chip tray, the first plate, the second plate, and the index tray between the consumable area and the work area. The stage aligns the first plate receptacle, the second plate receptacle, and the third plate receptacle with the contact dispenser and the non-contact dispenser, the non-contact dispenser being fluidly coupled to the reagent reservoir.

[0009] In a seventh implementation, an apparatus is provided that includes a system having a consumable area, a mover, a work area, a magnet, a thermocycler, an analyzer area, and a reagent reservoir receptacle for receiving a reagent reservoir. The consumable area includes a chip tray including a first chip and a second chip, a first plate having wells for containing samples, a second plate having wells, an index tray having wells for containing indexes, and a bead tray having wells for containing beads. The work area includes a contact dispenser, a non-contact dispenser, and a stage including a first plate receptacle, a second plate receptacle, and a third plate receptacle. The analyzer area includes a substrate and an imaging system. The mover moves the chip tray, the first plate, the second plate, and the index tray between the consumable area and the work area. The stage aligns the first plate receptacle, the second plate receptacle, and the third plate receptacle with respect to the contact dispenser and the non-contact dispenser.

[0010] In an eighth implementation, a modular system for preparing a library of samples for sequencing is provided, the modular system including a first assay bay, a common bay, and a mover. The first assay bay includes a first work area including a first contact dispenser, a work plate receptacle, a thermocycler, and a magnet, and a first drawer. The first drawer includes a consumable area adapted to receive a sample plate adapted to accommodate a sample, and a plurality of consumables for interacting with the sample. The common bay includes an analyzer area including an imaging system. The mover is operably coupled to the first assay bay and the common bay. The first contact dispenser is linearly movable in a first direction between the consumable area and the first work area, and is configured to (i) move a sample plate in the consumable area to a work plate in the first work area, and (ii) move a plurality of consumables between the consumable area and the sample plate in the first work area. The mover is movable between the first assay bay and the common bay in a first direction and a second direction perpendicular to the first direction, and is configured to move the sample plate from the first working area to the analyzer area for analysis by the imaging system.

[0011] In a ninth implementation, a modular bay for preparing a library of samples for sequencing is disclosed, the modular bay including a work area including a contact dispenser, a work plate receptacle, a thermocycler, and a magnet, and a drawer. The drawer includes a consumable area adapted to receive a sample plate adapted to contain a sample and a plurality of consumables for interacting with the sample. The contact dispenser is linearly movable longitudinally between the consumable area and the work area, and is configured to (i) move the sample plate in the consumable area to the work plate in the work area and (ii) move the plurality of consumables.

[0012] In a tenth implementation, an apparatus includes a pipette assembly including a body, a guide, a bar, a plurality of pipettes, a plurality of gaskets, and a pipette cam assembly. The body includes a base defining a plurality of pipette openings. The guide includes a plurality of protrusions defining pipette openings that align with the pipette openings of the base. The bar includes a plurality of openings through which the protrusions of the guide extend. The plurality of pipettes are coupled to the body and extend through the pipette openings of the body and the guide. Each pipette has an end including a flange. A plurality of gaskets are disposed between the corresponding flanges of the pipette and the protrusions. The pipette cam assembly moves the body away from the guide and moves the flanges of the pipettes toward the protrusions to compress the gasket, and moves the body toward the guide and moves the flanges of the pipettes away from the protrusions to relax the gasket.

[0013] In an eleventh implementation, an apparatus includes a thermocycler, a base, a plate receptacle, and a cover assembly. The base includes a stop wall, and the plate receptacle is on the base. The cover assembly is movably coupled to the base. The cover assembly has a sled, a cover, a cover follower, and a cam assembly. The sled includes a front wall, a rear wall, and a receptacle defined between the front and rear walls. The cover is disposed within the receptacle of the sled. The cover follower is disposed within the receptacle of the sled and movably coupled to the cover. The cam assembly moves the cover toward the base to cover the plate receptacle and moves the cover follower toward the base. The plate receptacle receives a plate having wells, and the thermocycler regulates the temperature of samples in the wells of the plate.

[0014] In a twelfth implementation, the device includes a drawer including a platform. The drawer includes a plate receptacle, a small liquid reagent well plate receptacle, a large liquid reagent well plate receptacle, a dry well plate receptacle, and a waste reservoir. The plate receptacle is coupled to the platform. The small liquid reagent well plate receptacle is coupled to the platform and includes a base, a first end wall, and a second end wall. The first end wall is coupled to the base and has an inwardly extending lip that forms a first groove with the base. The second end wall is coupled to the base and has an inwardly extending lip that forms a second groove with the base and includes a key. The large liquid reagent well plate receptacle is coupled to the platform and has a base, a first end wall, and a second end wall. The first end wall has an inwardly extending lip that forms a first groove with the base of the large liquid reagent well plate receptacle. The second end wall is coupled to the base and has an inwardly extending lip that forms a second groove with the base of the large liquid reagent well plate receptacle and includes a key. The dry well plate receptacle is positioned on the platform and defines a waste reservoir compartment. The waste reservoir has a wide portion that includes an inlet and a narrow portion that extends from the wide portion and is positioned within the waste reservoir compartment.

[0015] In a thirteenth implementation, an apparatus includes a reagent well plate and a plurality of reagent wells. The reagent well plate includes a first end wall including a male snap-fit ​​component, a second end wall including a male snap-fit ​​component, and a panel coupled to and extending between the first and second end walls. The panel defines a plurality of reagent well receptacles and includes a top surface. The reagent wells include ends having annular collars. The reagent wells are disposed within the reagent well receptacles, and the annular collars engage the top surface.

[0016] In a fourteenth implementation, an apparatus includes a well plate including a rectangular wall, a panel, and a plurality of reagent wells. The rectangular wall includes end walls and side walls. The end walls each include a notch and a recess that form a handle extending between the side walls. The panel is coupled to the rectangular wall. The panel defines a plurality of reagent well receptacles and includes a top surface. The end walls and side walls extend outward from the panel. The reagent wells include ends with annular collars. The reagent wells are disposed within the reagent well receptacles, and the annular collars engage the top surface.

[0017] In a fifteenth implementation, the device includes a consumable area, multiple assay bays, a common bay, and a cross-bay gantry. The consumable area is for carrying multiple well plates. Each of the well plates includes a rectangular wall including a cutout. Each of the assay bays includes an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing. The common bay includes a common bay plate receptacle and an imaging system for performing quantification processes associated with preparing a library of samples for sequencing. The cross-bay gantry includes grippers movable between the consumable area, the assay bays, and the common bay. The grippers include arms with inwardly extending extensions that are movable toward or away from each other. The gripper extensions are positionable within corresponding well plate notches to move the well plate between any of the consumable bays, assay bay plate receptacles, and common bay plate receptacles.

[0018] In a sixteenth implementation, an apparatus includes a library preparation system including a consumable area, multiple assay bays, a common bay, a cross-bay gantry, and a sample sipper assembly. The consumable area is for carrying multiple well plates. Each assay bay includes an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing. The common bay includes a common bay plate receptacle and an imaging system for performing quantification processes associated with preparing a library of samples for sequencing. The cross-bay gantry includes a gripper movable between the consumable area, the assay bays, and the common bay. The sample sipper assembly includes multiple shippers and an actuator for moving the shippers relative to the plate receptacles of the library preparation system. The sample sipper assembly is associated with transferring the library of samples to the sequencing system.

[0019] In a seventeenth implementation, the device includes multiple assay bays, a common bay, and a cross-bay gantry. Each assay bay includes an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing. The pipette assembly includes a body, a guide, a bar, multiple pipettes, multiple gaskets, and a pipette cam assembly. The body includes a base defining multiple pipette openings. The guide includes multiple protrusions defining pipette openings that align with the pipette openings of the base. The bar includes multiple openings through which the protrusions of the guide extend. The pipettes are coupled to the body and extend through the pipette openings of the body and the guide. Each pipette has an end including a flange. The gasket is disposed between the corresponding flange of the pipette and the protrusion. The pipette cam assembly is for moving the body away from the guide and moving the flange of the pipette toward the protrusion to compress the gasket, and for moving the body toward the guide and moving the flange of the pipette away from the protrusion to relax the gasket. The common bay includes a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of samples for sequencing. The cross-bay gantry includes a gripper movable between the assay bay and the common bay.

[0020] In an eighteenth implementation, an apparatus is provided that includes a plurality of assay bays, each assay bay including an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing, the thermocycler including a base including a stop wall, a plate receptacle on the base, and a cover assembly movably coupled to the base, the cover assembly including a sled including a front wall and a rear wall and a receptacle defined between the front wall and the rear wall, a cover disposed within the receptacle of the sled, and a sled. a cover follower disposed within the red receptacle and movably coupled to the cover, a cam assembly that moves the cover toward the base to cover the plate receptacle and moves the cover follower toward the base, the plate receptacle receives a plate having wells, the thermocycler adjusts the temperature of the samples in the wells of the plate, the common bay includes a common bay plate receptacle and an imaging system that performs a quantification process associated with preparing a library of samples for sequencing, and a cross bay gantry including a gripper that is movable between the assay bay and the common bay.

[0021] In a nineteenth implementation, an apparatus is provided that includes a plurality of assay bays, each assay bay including a drawer including a platform and a plate receptacle coupled to the platform, an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing, wherein the drawer includes the plate receptacle coupled to the platform, a small liquid reagent well plate receptacle coupled to the platform and including a base, a first end wall having an inwardly extending lip that forms a first groove with the base, a second end wall coupled to the base and having an inwardly extending lip that forms a second groove and including a key, and a large liquid reagent well plate receptacle coupled to the platform and including a base. The device includes a plate receptacle, a first end wall having an inwardly extending lip that forms a first groove with the base of the large liquid reagent well plate receptacle, a second end wall that is connected to the base and forms a second groove with the base of the large liquid reagent well plate receptacle and has an inwardly extending lip that includes a key, a dry well plate receptacle that is positioned on the platform and defines a waste reservoir compartment, a waste reservoir that has a wide portion that includes an inlet and a narrow portion that extends from the wide portion and is positioned within the waste reservoir compartment, a common bay that includes a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of samples for sequencing, and a cross bay gantry that includes a gripper that is movable between the assay bay and the common bay.

[0022] In a twentieth implementation, a library preparation system for preparing a library of samples for sequencing is provided, the library preparation system including: a work area for preparing a library of samples for genomic sequencing; a communication interface; and one or more processors communicatively coupled to the communication interface and configured to communicate with a sequencer via the communication interface by sending or receiving information related to the library of samples.

[0023] In a 21st implementation, a method for communicating between a library preparation system and a sequencer is provided, the method including preparing a library of samples for genomic sequencing by a library preparation system having a contact dispenser and a working area for interacting one or more consumables with the samples, and communicating with the sequencer by one or more processors in the library preparation system by sending or receiving information about the library of samples via a communication interface.

[0024] In a 22nd implementation, a method includes receiving a small liquid reagent well plate by a small liquid reagent well plate receptacle on a platform of a drawer, wherein a snap-fit ​​connection is formed when the small liquid reagent well plate receptacle receives the small liquid reagent well plate; receiving a large liquid reagent well plate by a large liquid reagent well plate receptacle coupled to the platform of the drawer, wherein a snap-fit ​​connection is formed when the large liquid reagent well plate receptacle receives the large liquid reagent well plate; and a dry well plate disposed on the platform and defining a waste reservoir compartment. The method includes receiving a dry reagent well plate through a receptacle, wherein a waste reservoir is positioned within the waste reservoir compartment, and receiving the drawer into one of a plurality of assay bays of a library preparation system, wherein the library preparation system includes an assay bay and a common bay, wherein the assay bays are for performing amplification processes and cleanup processes associated with preparing a library of samples for sequencing, respectively, and the common bay is for performing library quantification processes, library pooling processes, denaturation processes, and dilution processes associated with preparing a library of samples for sequencing.

[0025] In a 23rd implementation form, the method includes performing amplification and cleanup processes associated with preparing a library of samples for sequencing on samples contained in a well plate placed on a plate receptacle of a thermocycler on an assay bay of the library preparation system; using a gripper to remove the well plate from the plate receptacle of the thermocycler by placing the gripper in a notch in the well plate and moving the gripper away from the plate receptacle; using the gripper to move the well plate to a common bay of the library preparation system; and performing a library quantification process associated with preparing the library of samples for sequencing in the common bay.

[0026] In a 24th implementation, the method includes inserting an end of a pipette of a pipette assembly in an assay bay of the library preparation system and a gasket carried by the pipette into a pipette tip on a drawer of the assay bay, compressing the gasket of the pipette assembly to couple the pipette tip and the pipette assembly, using the pipette assembly and pipette tip to dispense reagents into a well plate on a plate receptacle in the assay bay, and performing an amplification process and a cleanup process in the plate receptacle.

[0027] In a 25th implementation, the method includes moving a sled of a cover assembly of the thermocycler toward a stop wall of the base of the thermocycler, a cover disposed in a receptacle of the sled, and a cover follower disposed in the receptacle of the sled and movably coupled to the cover; engaging the stop wall with a cover bearing coupled to the cover; engaging a rear wall of the sled with a cover follower bearing coupled to the cover follower; moving an inner slot bearing within an inner cam slot of an inner cam plate to move the cover in a direction covering the plate receptacle, wherein the inner slot bearing is coupled to the cover and the inner cam plate is coupled to the sled; and moving an outer slot bearing within an outer cam slot of an outer cam plate to move the cover follower toward the base, wherein the outer slot bearing is coupled to the cover follower and the outer cam plate is coupled to the plate.

[0028] In a 26th implementation, a method includes performing amplification and cleanup processes on samples in a well plate in multiple assay bays, each assay bay including an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing the amplification and cleanup processes; using a cross-bay gantry to move the samples from the assay bays to a common bay; performing a library quantification process on the samples in the common bay; and archiving a library of samples.

[0029] In a 27th implementation, a method includes performing amplification and cleanup processes on samples in a well plate in multiple assay bays, each assay bay including an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing the amplification and cleanup processes; using a cross-bay gantry to move the samples from the assay bays to a common bay; and performing library quantification and library pooling processes on the samples in the common bay.

[0030] In a 28th implementation, a method includes performing amplification and cleanup processes on samples in a well plate in multiple assay bays, each assay bay including an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing the amplification and cleanup processes; using a cross-bay gantry to move the samples from the assay bays to a common bay; and preparing a sequencing-ready pool of samples in the common bay.

[0031] In a 29th implementation, a method includes performing amplification and cleanup processes on samples in a well plate in multiple assay bays, each assay bay including an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet; using a cross-bay gantry to move the samples from the assay bays to a common bay; preparing a sequencing-ready pool of samples in the common bay; and transferring the sequencing-ready pool of samples to a sequencer.

[0032] In a thirtieth implementation, the apparatus includes a library preparation system that includes an assay bay for performing amplification and cleanup processes and a common bay for performing a quantification process.

[0033] In a 31st implementation form, an apparatus includes: a library preparation system including a sample sipper assembly including a sipper coupled to a sample cartridge; a sequencing instrument including a flow cell interface coupled to a flow cell having a plurality of channels; a central valve and an auxiliary waste line coupled to the central valve and coupled to a waste reservoir, wherein the central valve is coupled to the flow cell interface and is movable between a first position in which it fluidly connects the inlets of the plurality of flow paths to the auxiliary waste line and a second position in which it fluidly connects the reagent reservoir and the plurality of flow paths; and a sample loading assembly positioned between the flow cell interface and the sample sipper assembly of the library preparation system, the sample loading assembly including a body carrying a plurality of sample valves and defining a plurality of sample ports and a plurality of flow cell ports, each sample port being coupled to a corresponding sipper of the sample sipper assembly via a sample fluid line, wherein the sample sipper assembly of the library preparation system is positioned downstream of the flow cell interface of the sequencing instrument.

[0034] In a 32nd implementation form, an apparatus is provided that includes a library preparation system including a sample sipper assembly including a sipper coupled to a sample cartridge, a sequencing instrument, and one or more valves adapted to be coupled to corresponding reagent reservoirs, a flow cell interface adapted to be coupled to a flow cell, and a pump adapted to load a target sample into a channel of the flow cell via the flow cell interface associated with an outlet of the flow cell and the corresponding sipper of the sample sipper assembly.

[0035] In a 33rd implementation, the method includes moving a first sample valve of one or more sample valves to a first position to fluidically couple a first sipper of a sipper manifold assembly of the library preparation system to a first pump of the sequencing instrument, drawing a first target sample from the library preparation system through the first sipper of the sipper manifold assembly toward the first pump of the sequencing instrument, moving the first sample valve to a second position to fluidically couple the first pump to a channel of a flow cell coupled to a flow cell interface of the sequencing instrument, and pumping the first target sample into the first channel of the flow cell through an outlet of the first channel.

[0036] In a 34th implementation, the method includes priming the fluid lines and sample sipper assembly of a library preparation system with a read buffer using a pump manifold assembly of a sequencing instrument; drawing a target sample from the library preparation system into the fluid lines and the sequencing instrument using the sample sipper assembly and pump manifold assembly; drawing a lag buffer from the library preparation system into the fluid lines and behind the target sample and sequencing instrument using the sample sipper assembly and pump manifold assembly; and forcing the lag buffer, target sample, and read buffer toward a channel of a flow cell positioned on a flow cell interface of the sequencing instrument.

[0037] Furthermore, depending on the first to thirty-fourth implementation forms described above, the apparatus and / or method may further include or comprise any one or more of the following: In one implementation, the first contact dispenser is not movable in the second direction.

[0038] In another implementation, both the first contact dispenser and the mover are movable in a third direction perpendicular to the first and second directions. In another implementation, the common bay includes a pooling area, and the mover is configured to move between the analyzer area and the pooling area.

[0039] In another implementation, the first contact dispenser includes a first contact head configured to hold a tip. In another implementation, the first drawer is movable linearly in a first direction relative to the first work area between a loading position and an operating position, and when the first drawer is in the loading position, the first drawer is spaced a first distance from the first work area, and when the first drawer is in the operating position, the first drawer is spaced a second distance from the first work area, the second distance being less than the first distance.

[0040] In another implementation, the apparatus includes a movable stage coupled to the first contact dispenser for linearly moving the first contact dispenser in a first direction and a third direction. In another implementation, the apparatus includes a first actuator operably coupled to the movable stage and the magnet, the first actuator configured to actuate movement of the movable stage to move the magnet relative to the work plate receptacle.

[0041] In another implementation, the apparatus includes a gantry system, and the mover is movable along the gantry system. In another implementation, the apparatus includes a second actuator configured to actuate movement of the mover in the first direction and the second direction.

[0042] In another implementation, the apparatus includes a door that is movable to enclose the thermocycler and the work plate receptacle. In another implementation, the thermocycler is aligned with the work plate receptacle in a first orientation.

[0043] In another implementation, the thermocycler is configured to amplify samples in a working plate. In another implementation, the consumable area is adapted to receive a lid for the work plate, and the first contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

[0044] In another implementation, the plurality of consumables include a tip tray including a first reusable tip and a second reusable tip, a second work plate, an index tray adapted to accommodate an index, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate a reagent.

[0045] In another implementation, the first contact dispenser is configured to use a first reusable tip to transfer a sample from a sample plate in the consumable area to a work plate in the first work area, and to use a second reusable tip to transfer one or more indexes from an index tray in the consumable area to the work plate.

[0046] In another implementation, the first contact dispenser is configured to aspirate an index from an index tray in the consumable area and dispense the index into a work plate in the first work area.

[0047] In another implementation, the first contact dispenser is configured to aspirate beads from a bead tray in the consumable area and dispense the beads into a work plate in the first work area.

[0048] In another implementation, the magnet is movable toward the work plate receptacle to attract beads in the work plate toward the magnet, and the first contact dispenser is configured to aspirate a first reagent from a reagent reservoir in the consumable area and dispense the first reagent into the work plate.

[0049] In another implementation, the first contact dispenser is configured to aspirate the sample and the first reagent from the work plate, the mover is configured to move the work plate to the consumable area and move a second work plate in the consumable area to a work plate receptacle in the first work area, and the first contact dispenser is configured to dispense the sample and the first reagent into the second work plate.

[0050] In another implementation, the mover is configured to move the second working plate from the first working area to the analyzer area. In another implementation, the imaging system is configured to acquire image data of the portion of the first reagent and the sample and determine a concentration of the sample.

[0051] In another implementation, the device includes a second assay bay arranged parallel to the first assay bay and including a second contact dispenser, a second work area including a work plate receptacle adapted to receive a work plate, a thermocycler, and a magnet, and a second drawer. The second drawer includes a second consumable area adapted to receive a sample plate adapted to contain a sample and a plurality of consumables for interacting with the sample in the working plate in the second working area, a mover is operably coupled to the second assay bay, and the second contact dispenser is linearly movable in a first direction between the consumable area and the second working area, thereby configured to (i) move a sample from the sample plate in the second consumable area to the working plate in the second working area and (ii) move a plurality of consumables between the second consumable area and the working plate in the second working area, and the mover is movable in the first direction and the second direction between the second assay bay and the common bay, thereby configured to move the working plate from the second working area to the analyzer area for analysis by the imaging system.

[0052] In another implementation, the second workflow is executed concurrently with the first workflow. In another implementation, the device includes a sequencer and a plurality of fluid lines fluidly coupling the common bay and the sequencer such that prepared samples automatically flow from the common bay to the sequencer.

[0053] In another implementation, the common bay includes a sipper assembly having multiple sippers, the sequencer includes multiple flow cells, and multiple fluid lines fluidly couple the multiple sipper to the multiple flow cells.

[0054] In another implementation, a contact dispenser includes a contact head configured to hold a tip. In another implementation, the drawer is movable linearly longitudinally relative to the work area between a loading position and an operating position, and when the drawer is in the loading position, the drawer is spaced a first distance from the work area, and when the drawer is in the operating position, the drawer is spaced a second distance from the work area, the second distance being less than the first distance.

[0055] In another implementation, the contact dispenser is not movable laterally perpendicular to the longitudinal direction. In another implementation, the apparatus includes a movable stage operatively coupled to the contact dispenser for linearly moving the contact dispenser longitudinally.

[0056] In another implementation, the apparatus includes an actuator configured to actuate movement of the movable stage in the longitudinal direction. In another implementation, the apparatus includes a door that is movable to enclose the thermocycler and the work plate receptacle.

[0057] In another implementation, the thermocycler is longitudinally aligned with the work plate receptacle. In another implementation, the thermocycler is configured to amplify samples in a working plate.

[0058] In another implementation, the consumable area is adapted to receive a lid for the work plate, and the contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

[0059] In another implementation, the plurality of consumables include a tip tray including a first reusable tip and a second reusable tip, a second work plate, an index tray adapted to accommodate an index, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate a reagent.

[0060] In another implementation, the contact dispenser is configured to use a first reusable tip to transfer a sample from a sample plate in the consumable area to a work plate in the work area, and to use a second reusable tip to transfer one or more indexes from an index tray in the consumable area to the work plate.

[0061] In another implementation, the contact dispenser is configured to aspirate the index from an index tray in the consumable area and dispense the index into a work plate in the work area.

[0062] In another implementation, the contact dispenser is configured to aspirate beads from a bead tray in the consumable area and dispense the beads into a work plate in the work area.

[0063] In another implementation, the magnet is movable toward the work plate receptacle to attract beads in the work plate toward the magnet, and the contact dispenser is configured to aspirate a first reagent from a reagent reservoir in the consumable area and dispense the first reagent into the work plate.

[0064] In another implementation, the contact dispenser is configured to aspirate the sample and the first reagent from the work plate, the mover is configured to move the work plate to the consumable area and move a second work plate in the consumable area to a work plate receptacle in the work area, and the contact dispenser is configured to dispense the sample and the first reagent into the second work plate.

[0065] In another implementation, the device includes an actuator for moving the magnet relative to the plate receptacle. In another implementation, the thermocycler is aligned with the plate receptacle.

[0066] In another implementation, the mover moves the first plate from the consumable area to the plate receptacle. In another implementation, the stage aligns the contact dispenser with a chip tray, the contact dispenser couples with a first chip from the chip tray, the stage aligns the contact dispenser with an index tray, the contact dispenser aspirates an index from the index tray, the stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses the index into a well of the first plate.

[0067] In another implementation, the thermocycler amplifies the samples in the wells of the first plate. In another implementation, the consumable area further includes a lid, and the mover moves the lid from the consumable area and places the lid on the first plate to cover the wells of the first plate.

[0068] In another implementation, the mover moves the lid from the first plate to the consumable area. In another implementation, the stage aligns the contact dispenser with a bead tray, and the contact dispenser aspirates beads from the bead tray, and the stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses beads into wells of the first plate.

[0069] In another implementation, the stage aligns a contact dispenser with a first plate, and the contact dispenser dispenses a first reagent into the wells of the first plate. In another implementation, the stage aligns the contact dispenser with the chip tray, the contact dispenser places a first chip into the chip tray, and the contact dispenser mates with a second chip from the chip tray.

[0070] In another implementation, the actuator moves a magnet toward the plate receptacle, attracting beads toward the magnet, and the stage aligns the contact dispenser with the first plate, allowing the contact dispenser to aspirate the first reagent from the wells.

[0071] In another implementation, the system includes a waste material, and the contact dispenser dispenses the first reagent into the waste material. In another implementation, the stage aligns a contact dispenser with the first plate, and the contact dispenser dispenses the second reagent into the wells of the first plate.

[0072] In another implementation, the actuator moves a magnet toward the plate receptacle to attract beads toward the magnet, the stage aligns the contact dispenser with the first plate to allow the contact dispenser to aspirate a second reagent and sample from the wells of the first plate, and the stage aligns the contact dispenser with the second plate to allow the contact dispenser to dispense the second reagent and sample into the wells of the second plate.

[0073] In another implementation, an imaging system acquires image data of a portion of the second reagent and the sample, and the system determines the concentration of the sample. In another implementation, the device includes a second contact dispenser.

[0074] In another implementation, the stage aligns a second plate with a second contact dispenser, which dispenses a diluent into the wells of the second plate to dilute the sample based on the determined concentration of the sample.

[0075] In another implementation, a system includes a first work area including a contact dispenser, a stage that moves the contact dispenser, a plate receptacle, a magnet, and a thermocycler.

[0076] In another implementation, the system includes a second work area including a mover, a second contact dispenser, a plate receptacle, and an analyzer including an imaging system. In another implementation, the system includes a loading area.

[0077] In another implementation, the loading area includes a shipper assembly. In another implementation, the sipper assembly includes a sample sipper assembly. In another implementation, the loading area includes a plate receptacle.

[0078] In another implementation, the loading area includes a stage for moving the plate receptacle relative to the shipper assembly. In another implementation, the apparatus includes a second system.

[0079] In another implementation, a second system is fluidly coupled to the system. In another implementation, the second system includes a sequencing instrument. In another implementation, the apparatus further includes an actuator for moving the magnet relative to the second plate receptacle.

[0080] In another implementation, the device further includes a door movable to enclose the reagent reservoir receptacle. In another implementation, the device further includes a gas source fluidly coupled to the reagent reservoir.

[0081] In another implementation, the device further includes a valve for controlling the flow of gas from the gas source to the reagent reservoir receptacle. In another implementation, the gas includes nitrogen.

[0082] In another implementation, the thermocycler is aligned with a second plate receptacle. In another implementation, the thermocycler is carried by a stage.

[0083] In another implementation, the mover moves the tip tray from the consumable area to the first plate receptacle, the mover moves the first plate from the consumable area to the second plate receptacle, and the mover moves the index tray from the consumable area to the third plate receptacle.

[0084] In another implementation, the stage aligns the contact dispenser with a chip tray, the contact dispenser couples with a first chip from the chip tray, the stage aligns the contact dispenser with an index tray, the contact dispenser aspirates an index from the index tray, the stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses the index into a well of the first plate.

[0085] In another implementation, the thermocycler amplifies the samples in the wells of the first plate. In another implementation, the consumable area further includes a lid, and the mover moves the lid from the consumable area and places the lid on the first plate to cover the wells of the first plate.

[0086] In another implementation, the mover moves the lid from the first plate to the consumable area. In another implementation, the mover moves the index tray from the third receptacle to the consumable area.

[0087] In another implementation, the mover moves the bead tray from the consumable area to a third plate receptacle. In another implementation, the stage aligns the contact dispenser with a bead tray, and the contact dispenser aspirates beads from the bead tray. The stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses beads into wells of the first plate.

[0088] In another implementation, the stage aligns a non-contact dispenser with the first plate, and the non-contact dispenser dispenses a first reagent from a reagent reservoir into the wells of the first plate.

[0089] In another implementation, the stage aligns the contact dispenser with the chip tray, and the contact dispenser places a first chip into the chip tray, and the contact dispenser mates with a second chip from the chip tray.

[0090] In another implementation, the actuator moves the magnet toward the second plate receptacle, attracting the beads toward the magnet, and the stage aligns the contact dispenser with the first plate, allowing the contact dispenser to aspirate the first reagent from the wells.

[0091] In another implementation, the system includes a waste material, and the contact dispenser dispenses the first reagent into the waste material. In another implementation, the mover moves the bead tray from the third plate receptacle to the consumable area.

[0092] In another implementation, the stage aligns a non-contact dispenser with the first plate, and the non-contact dispenser dispenses a second reagent from a reagent reservoir into the wells of the first plate.

[0093] In another implementation, the mover moves the second plate from the consumable area to a third plate receptacle. In another implementation, the actuator moves the magnet toward the second plate receptacle to attract the beads toward the magnet, the stage aligns the contact dispenser with the first plate to allow the contact dispenser to aspirate the second reagent and sample from the wells of the first plate, and the stage aligns the contact dispenser with the second plate to allow the contact dispenser to dispense the second reagent and sample into the wells of the second plate.

[0094] In another implementation, the stage aligns the contact dispenser with the chip tray, and the contact dispenser places the second chip into the chip tray and mates with the first chip from the chip tray.

[0095] In another implementation, the analyzer area substrate is carried by a stage, and the substrate includes a pair of plates defining a gap between them. In another implementation, the substrate includes an inlet and an outlet in fluid communication with the gap.

[0096] In another implementation, the substrate further includes a seal disposed between the pair of plates and defining a channel between the inlet and the outlet. In another implementation, the apparatus further includes a waste reservoir fluidly coupled to the outlet of the substrate.

[0097] In another implementation, the stage aligns the contact dispenser with a second plate, the contact dispenser aspirates a portion of the second reagent and sample from a well of the second plate, and the stage aligns the contact dispenser with an inlet of the substrate, allowing the contact dispenser to dispense a portion of the second reagent and sample into the inlet of the substrate.

[0098] In another implementation, an imaging system acquires image data of a portion of the second reagent and the sample, and the system determines the concentration of the sample. In another implementation, the stage aligns the second plate with a non-contact dispenser, which dispenses diluent into the wells of the second plate to dilute the sample based on the determined concentration of the sample.

[0099] In another implementation, the thermocycler is positioned below the second plate receptacle. In another implementation, the second plate receptacle includes a thermal block that defines a well receptacle, and the thermocycler is disposed below the well receptacle.

[0100] In another implementation, the apparatus further includes a heat sink coupled to the thermocycler. In another implementation, the apparatus includes a lid and an actuator, the actuator moving the lid relative to the plate receptacle to cover the plate receptacle.

[0101] In another implementation, a gasket that is compressed when the end of the pipette is placed into the pipette tip allows the gasket to form a bond with the pipette tip. In another implementation, a gasket that is relaxed when the end of the pipette is placed into the pipette tip allows the pipette tip to be uncoupled from the pipette.

[0102] In another implementation, the guide includes an outward channel and the bar includes a first arm and a second arm that extend into the outward channel of the guide. In another implementation, the bar includes a first arm and a second arm, and the pipette cam assembly includes a guide bearing coupled to the guide, a bar bearing coupled to the corresponding first arm and second arm, and a cam shaft including an inner lobe that engages the guide bearing and an outer lobe that engages the bar bearing.

[0103] In another implementation, engagement of the inner lobe of the camshaft with the guide bearing moves the body away from the guide and moves the flange of the pipette towards the protrusion to compress the gasket.

[0104] In another implementation, the inner lobe of the camshaft engaging the guide bearing in the second position allows the guide to move toward the bar and move the flange of the pipette away from the protrusion, loosening the gasket.

[0105] In another implementation, an outer lobe of the camshaft that engages the burr bearing moves the burr toward a flange of the pipette, allowing the burr to engage a pipette tip carried by the pipette and urge the pipette tip to be released from the pipette assembly.

[0106] In another implementation, one of the bar bearings faces one of the guide bearings. In another implementation, the apparatus includes a torsion bar spring disposed between the bar and the guide for biasing the bar bearing toward the corresponding outer lobe.

[0107] In another implementation, the device includes a guide spring disposed between the body and the guide for biasing the body away from the guide. In another implementation, the body includes a first side and a second side, the camshaft includes a first camshaft portion and a second camshaft portion, the first camshaft portion coupled to the first side of the body, and the second camshaft portion coupled to the second side of the body.

[0108] In another implementation, the first camshaft portion is spaced apart from the second camshaft portion. In another implementation, the apparatus includes a motor and a gear set, the gear set coupled to the camshaft.

[0109] In another implementation, the movement of the motor rotates a camshaft. In another implementation, the gear set includes first and second gears, first and second pinions, and a shaft coupling the first and second pinions.

[0110] In another implementation, the body includes a first side and a second side, the first gear is coupled to the first side of the body and to inner and outer lobes on the first side of the body, and the second gear is coupled to the second side of the body and to inner and outer lobes on the second side of the body.

[0111] In another implementation, the first and second sides of the body define a shaft opening, and the shaft is rotatably coupled within the shaft opening. In another implementation, the shaft is spaced apart from the pipette.

[0112] In another implementation, the body includes a first side and a second side and a wall defining a receptacle, the pipette being disposed within the receptacle. In another implementation, the pipettes each include a barrel, and the device includes a plurality of pistons disposed within the corresponding barrels and movable within the barrels.

[0113] In another implementation, the device includes an actuator coupled to the piston to move the piston between a retracted position and an extended position within the barrel. In another implementation, the actuator includes a ball screw.

[0114] In another implementation, the actuator includes a pair of linear rails and a lift, the lift coupled to the piston and the linear rails and movable by a ball screw. In another implementation, the lift is C-shaped and has ends, and the apparatus includes a carriage coupled to a corresponding end of the lift and coupled to the linear rail.

[0115] In another implementation, the cam assembly includes an inner cam plate, an outer cam plate, a cover bearing, an inner slot bearing, a cover follower bearing, and an outer slot bearing. The inner cam plates are coupled to the sled and each define an inner cam slot. The outer cam plates are coupled to the base and each define an outer cam slot. The cover bearings are coupled to the cover and positioned to engage the stop wall. The inner slot bearings are coupled to the cover and movably positioned within the inner cam slot. The cover follower bearings are coupled to the cover follower and positioned to engage the rear wall of the sled. The outer slot bearings are coupled to the cover follower and movably positioned within the outer cam slot.

[0116] In another implementation, the cover bearing engages the stop wall, causing the inner slot bearing to move within the inner cam slot and the cover bearing to move along the stop wall, moving the cover toward the base and covering the plate receptacle.

[0117] In another implementation, the cover follower bearing engages the rear wall, causing the outer slot bearing to move within the outer cam slot, causing the cover follower bearing to move along the rear wall and move the cover follower toward the base.

[0118] In another implementation, the device includes a spring that biases the cover away from the cover follower. In another implementation, the apparatus includes a guide rod that movably couples the cover and the cover follower.

[0119] In another implementation, the cover includes a blind hole, the cover follower includes a through hole, and the guide rod is disposed within the corresponding blind hole in the cover and within the through hole in the cover follower. In another implementation, the spring surrounds a corresponding guide rod.

[0120] In another implementation, the cover defines a cover bearing receptacle in which the cover bearing is disposed. In another implementation, the cover follower defines a cover follower bearing receptacle in which the cover follower bearing is disposed.

[0121] In another implementation, the apparatus includes a linear rail coupled to the base and a carriage coupled to the back wall and coupled to the linear rail. In another implementation, the stop wall includes extensions with an opening defined therebetween, and the front wall is sized to pass between the extensions.

[0122] In another implementation, the cover bearing engages the extension. In another implementation, the device includes a magnet and an actuator, the actuator moving the magnet relative to the plate receptacle.

[0123] In another implementation, the device includes a central well plate support wall extending from the base and positioned between first and second end walls of the miniature liquid reagent well plate receptacle. In another implementation, the device includes a central well plate support wall extending from the base and positioned between first and second end walls of the large liquid reagent well plate receptacle.

[0124] In another implementation, the small liquid reagent well plate receptacle is positioned between the plate receptacle and the large liquid reagent well plate receptacle. In another implementation, the large liquid reagent well plate receptacle is positioned between the small liquid reagent well plate receptacle and the dry well plate receptacle.

[0125] In another implementation, the dry well plate receptacle is positioned between the large liquid reagent well plate receptacle and the wide portion of the waste reservoir that includes the inlet. In another implementation, the inlet includes a rectangular inlet for receiving waste associated with a multi-tip pipette.

[0126] In another implementation, the drawer further includes a tip receptacle. In another implementation, the tip receptacle is positioned between the large liquid reagent well plate receptacle and the dry well plate receptacle.

[0127] In another implementation, the first end wall includes a keying notch. In another implementation, the device includes an impermeable barrier coupled to the end of the reagent well. In another implementation, the device includes machine-readable code coupled to the panel.

[0128] In another implementation, the reagent well plate includes a miniature liquid reagent well plate. In another implementation, the first end wall and the second end wall extend outwardly from the panel. In another implementation, the panel is concave.

[0129] In another implementation, the panel is substantially flat when the first end wall and the second end wall are coupled to the reagent well plate receptacle. In another implementation, each of the reagent wells includes a second annular collar longitudinally spaced from the first annular collar, and the panel is disposed between the annular collar and the second annular collar of the corresponding reagent well.

[0130] In another implementation, the panel includes a plurality of second reagent well receptacles having a different size than the reagent well receptacle, the second reagent well receptacles being disposed between the second end wall and the reagent well receptacle.

[0131] In another implementation, the device includes a bulk reagent well disposed within the second reagent well receptacle. In another implementation, the device includes an L-tab coupled to each of the bulk reagent wells.

[0132] In another implementation, the L-tab includes a first leg coupled to the bulk reagent well and a second leg extending from the first leg at an angle corresponding to the angle of the second end wall. In another implementation, the L-tabs are positioned within the dimensional envelope of the reagent well plate.

[0133] In another implementation, the second end wall includes a first wall section and a second wall section coupled to one another to form a recess. In another implementation, the L-tab is positioned within the dimensional envelope of the recess.

[0134] In another implementation, the first end wall includes a pair of first end wall portions and a pair of male snap-fit ​​components, each of the first end wall portions including one of the male snap-fit ​​components.

[0135] In another implementation, the second end wall includes a pair of second end wall portions and a pair of male snap-fit ​​components, each of the second end wall portions including one of the male snap-fit ​​components.

[0136] In another implementation, the device includes multiple impermeable barriers, each of the reagent wells being covered by one of the impermeable barriers. In another implementation, each of the reagent wells includes a second annular collar longitudinally spaced from the annular collar, and a snap-fit ​​connection is formed between the plate, the annular collar, and the second annular collar.

[0137] In another implementation, the male snap-fit ​​component includes a tapered tab. In another implementation, the notches and recesses in adjacent plates form the openings. In another implementation, the end wall includes a handle that forms a dogbone shape.

[0138] In another implementation, the rectangular wall and the panel form a step. In another implementation, the rectangular wall includes ends that form openings sized to receive steps of adjacent well plates.

[0139] In another implementation, the panel includes multiple rows of reagent well receptacles. In another implementation, the panel includes an array of reagent well receptacles. In another implementation, a device includes a lid including a lid rectangular wall and a lid panel, the lid rectangular wall including a lid end wall and a lid side wall, the lid end walls each including a lid cutout forming a lid handle extending between the lid side walls.

[0140] In another implementation, the lid cutout and adjacent plate form an opening. In another implementation, the lid rectangular wall and the lid panel form a lid step. In another implementation, the lid rectangular wall includes edges that form a lid opening sized to receive a lid step of an adjacent lid.

[0141] In another implementation, the rectangular wall and panel form a step, and the lid opening is sized to receive the step of an adjacent well plate. In another implementation, the apparatus includes a fluid line fluidly coupling a sipper of the sample sipper assembly and a sequencing instrument.

[0142] In another implementation, the device includes a loading area that includes a sample sipper assembly and a plate receptacle. In another implementation, the loading area includes a stage for moving the plate receptacle relative to the sample sipper assembly.

[0143] In another implementation, a gasket that is compressed when the end of the pipette is placed into the pipette tip allows the gasket to form a bond with the pipette tip. In another implementation, a gasket that is relaxed when the end of the pipette is placed into the pipette tip allows the pipette tip to be uncoupled from the pipette.

[0144] In another implementation, the guide includes an outward channel and the bar includes a first arm and a second arm that extend into the outward channel of the guide. In another implementation, the bar includes a first arm and a second arm, and the pipette cam assembly includes a guide bearing coupled to the guide, a bar bearing coupled to the corresponding first arm and second arm, and a cam shaft including an inner lobe that engages the guide bearing and an outer lobe that engages the bar bearing.

[0145] In another implementation, engagement of the inner lobe of the camshaft with the guide bearing moves the body away from the guide and moves the flange of the pipette towards the protrusion to compress the gasket.

[0146] In another implementation, the inner lobe of the camshaft engaging the guide bearing in the second position allows the guide to move toward the bar and move the flange of the pipette away from the protrusion, relaxing the gasket.

[0147] In another implementation, an outer lobe of the camshaft that engages the burr bearing moves the burr toward a flange of the pipette, allowing the burr to engage a pipette tip carried by the pipette and urge the pipette tip to be released from the pipette assembly.

[0148] In another implementation, one of the bar bearings faces one of the guide bearings. In another implementation, the apparatus includes a torsion bar spring disposed between the bar and the guide for biasing the bar bearing toward the corresponding outer lobe.

[0149] In another implementation, the device includes a guide spring disposed between the body and the guide for biasing the body away from the guide. In another implementation, the body includes a first side and a second side, and the camshaft includes a first camshaft portion and a second camshaft portion, wherein the first camshaft portion is coupled to the first side of the body and the second camshaft portion is coupled to the second side of the body.

[0150] In another implementation, the first camshaft portion is spaced apart from the second camshaft portion. In another implementation, the apparatus includes a motor and a gear set, the gear set coupled to the camshaft.

[0151] In another implementation, the movement of the motor rotates a camshaft. In another implementation, the gear set includes first and second gears, first and second pinions, and a shaft coupling the first and second pinions.

[0152] In another implementation, the body includes a first side and a second side, the first gear is coupled to the first side of the body and to inner and outer lobes on the first side of the body, and the second gear is coupled to the second side of the body and to inner and outer lobes on the second side of the body.

[0153] In another implementation, the first and second sides of the body define a shaft opening, and the shaft is rotatably coupled within the shaft opening. In another implementation, the shaft is spaced apart from the pipette.

[0154] In another implementation, the body includes a first side and a second side and a wall defining a receptacle, the pipette being disposed within the receptacle. In another implementation, the pipettes each include a barrel, and the device includes a plurality of pistons disposed within the corresponding barrels and movable within the barrels.

[0155] In another implementation, the device includes an actuator coupled to the piston to move the piston between a retracted position and an extended position within the barrel. In another implementation, the actuator includes a ball screw.

[0156] In another implementation, the actuator includes a pair of linear rails and a lift, the lift coupled to the piston and the linear rails and movable by a ball screw. In another implementation, the lift is C-shaped and has ends, and the apparatus includes a carriage coupled to a corresponding end of the lift and coupled to the linear rail.

[0157] In another implementation, the apparatus includes a sample sipper assembly including a plurality of sipper(s) and an actuator for moving the sipper(s) relative to the well plate, the sample sipper assembly being associated with transferring a library of samples to a sequencing system.

[0158] In another implementation, the cam assembly includes inner cam plates coupled to the sled, each defining an inner cam slot, outer cam plates coupled to the base, each defining an outer cam slot, a cover bearing coupled to the cover and positioned to engage the stop wall, an inner slot bearing coupled to the cover and movably disposed in the inner cam slot, a cover follower bearing coupled to the cover follower and positioned to engage the rear wall of the sled, and an outer slot bearing coupled to the cover follower and movably disposed in the outer cam slot.

[0159] In another implementation, the cover bearing engages the stop wall, causing the inner slot bearing to move within the inner cam slot and the cover bearing to move along the stop wall, moving the cover toward the base and covering the plate receptacle.

[0160] In another implementation, the cover follower bearing engages the rear wall, causing the outer slot bearing to move within the outer cam slot, causing the cover follower bearing to move along the rear wall and move the cover follower toward the base.

[0161] In another implementation, the device includes a spring that biases the cover away from the cover follower. In another implementation, the apparatus includes a guide rod that movably couples the cover and the cover follower.

[0162] In another implementation, the cover includes a blind hole, the cover follower includes a through hole, and the guide rod is disposed within the corresponding blind hole in the cover and within the through hole in the cover follower. In another implementation, the spring surrounds a corresponding guide rod.

[0163] In another implementation, the cover defines a cover bearing receptacle in which the cover bearing is disposed. In another implementation, the cover follower defines a cover follower bearing receptacle in which the cover follower bearing is disposed.

[0164] In another implementation, the apparatus includes a linear rail coupled to the base and a carriage coupled to the back wall and coupled to the linear rail. In another implementation, the stop wall includes extensions with an opening defined therebetween, and the front wall is sized to pass between the extensions.

[0165] In another implementation, the cover bearing engages the extension. In another implementation, the device includes an actuator that moves the magnet relative to the plate receptacle.

[0166] In another implementation, the device includes a central well plate support wall extending from the base and positioned between first and second end walls of the miniature liquid reagent well plate receptacle. In another implementation, the device includes a central well plate support wall extending from the base and positioned between first and second end walls of the large liquid reagent well plate receptacle.

[0167] In another implementation, the small liquid reagent well plate receptacle is positioned between the plate receptacle and the large liquid reagent well plate receptacle. In another implementation, the large liquid reagent well plate receptacle is positioned between the small liquid reagent well plate receptacle and the dry well plate receptacle.

[0168] In another implementation, the dry well plate receptacle is positioned between the large liquid reagent well plate receptacle and the wide portion of the waste reservoir that includes the inlet. In another implementation, the inlet includes a rectangular inlet for receiving waste associated with a multi-tip pipette.

[0169] In another implementation, the drawer further includes a tip receptacle. In another implementation, the tip receptacle is positioned between the large liquid reagent well plate receptacle and the dry well plate receptacle.

[0170] In another implementation, to communicate with the sequencer, the one or more processors are configured to send identification information of the library of samples to the sequencer via the communication interface.

[0171] In another implementation, to communicate with the sequencer, the one or more processors are configured to send one or more execution parameters for sequencing the library of samples to the sequencer via the communication interface.

[0172] In another implementation, the one or more processors are configured to send an indication of the preparation status of the library of samples to the sequencer via the communication interface.

[0173] In another implementation, to communicate with the sequencer, the one or more processors are configured to send instructions to the sequencer via the communication interface indicating a particular lane of the flow cell through which the sequencer should sequence a particular sample of the sample library.

[0174] In another implementation, to communicate with the sequencer, the one or more processors are configured to receive status information from the sequencer via a communication interface.

[0175] In another implementation, to communicate with the sequencer, the one or more processors are configured to receive an indication from the sequencer via the communication interface that the sequencer is ready to receive a library of samples.

[0176] In another implementation, the library preparation system includes a fluid line configured to be coupled to the library preparation system and a sequencer, wherein the library preparation system sends the library of samples to the sequencer via the fluid line in response to receiving an indication that the sequencer is ready to receive the library of samples.

[0177] In another implementation, the work area includes a work plate and a thermocycler. In another implementation, a library preparation system includes a contact dispenser and a drawer, the drawer including a consumable area adapted to receive a sample plate adapted to contain a sample and a plurality of consumables for interacting with the sample, the contact dispenser configured to (i) move the sample plate in the consumable area to a work plate in the work area, and (ii) move the plurality of consumables.

[0178] In another implementation, the communication interface includes a wired communication link attached to the library preparation system and the sequencer. In another implementation, communicating with the sequencer includes transmitting, by the one or more processors, identification information of the library of samples to the sequencer via the communication interface.

[0179] In another implementation, communicating with the sequencer includes sending, by the one or more processors, one or more execution parameters for sequencing the library of samples to the sequencer via the communication interface.

[0180] In another implementation, communicating with the sequencer includes sending, by the one or more processors, an indication of the preparation status of the library of samples to the sequencer via the communication interface.

[0181] In another implementation, communicating with the sequencer includes sending, by the one or more processors, instructions to the sequencer via the communication interface indicating a particular lane of the flow cell for the sequencer to sequence a particular sample of the sample library.

[0182] In another implementation, communicating with the sequencer includes receiving, at the one or more processors, status information from the sequencer via a communication interface. In another implementation, communicating with the sequencer includes receiving, at the one or more processors, an indication from the sequencer via the communication interface that the sequencer is ready to receive the library of samples.

[0183] In another implementation, the method includes, in response to receiving an indication that the sequencer is ready to receive the library of samples, sending, by the library preparation system, the library of samples to the sequencer via fluid lines coupled to the library preparation system and the sequencer.

[0184] In another implementation, the communication interface includes a wired communication link attached to the library preparation system and the sequencer. In another implementation, each assay bay includes an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for performing amplification and cleanup processes associated with preparing a library of samples for sequencing.

[0185] In another implementation, a small liquid reagent well plate includes a first end wall including a male snap-fit ​​component, a second end wall including a male snap-fit ​​component, a panel coupled to and extending between the first and second end walls, and a plurality of reagent wells disposed within the reagent well receptacles.

[0186] In another implementation, a small liquid reagent well plate receptacle includes a base, a first end wall having an inwardly extending lip that forms a first groove with the base, and a second end wall coupled to the base, having an inwardly extending lip that forms a second groove with the base, and including a key.

[0187] In another implementation, receiving the small liquid reagent well plate by the small liquid reagent well plate receptacle on the platform of the drawer includes a keying notch in the small liquid reagent well plate receiving a key in the small liquid reagent well plate receptacle.

[0188] In another implementation, a large liquid reagent well plate includes a first end wall including a male snap-fit ​​component, a second end wall coupled to the base and including a male snap-fit ​​component, a panel coupled to and extending between the first and second end walls, and a plurality of reagent wells disposed within the reagent well receptacles.

[0189] In another implementation, a large liquid reagent well plate receptacle includes a base, a first end wall coupled to the base and having an inwardly extending lip that forms a first groove with the base, and a second end wall coupled to the base and having an inwardly extending lip that forms a second groove with the base, the second end wall including a key.

[0190] In another implementation, receiving the large liquid reagent well plate by the large liquid reagent well plate receptacle on the platform of the drawer includes a keying notch in the large liquid reagent well plate receiving a key in the large liquid reagent well plate receptacle.

[0191] In another implementation, receiving the small liquid reagent well plate by the small liquid reagent well plate receptacle on the platform of the drawer includes supporting a panel of the small liquid reagent well plate using a central well plate support wall extending from the base of the small liquid reagent well plate receptacle and positioned between a first end wall and a second end wall of the small liquid reagent well plate receptacle.

[0192] In another implementation, supporting a panel of a miniature liquid reagent well plate includes supporting the panel using a plurality of central well plate support walls of a miniature liquid reagent well plate receptacle.

[0193] In another implementation, the panel of the small liquid reagent well plate supported by the central well plate of the small liquid reagent well plate receptacle allows the panel of the small liquid reagent well plate to be substantially flat.

[0194] In another implementation, the coupling between the miniature liquid reagent well plate and the miniature liquid reagent well plate receptacle allows the panel of the miniature liquid reagent well plate to be substantially flat.

[0195] In another implementation, receiving the large liquid reagent well plate by the large liquid reagent well plate receptacle on the platform of the drawer includes supporting a panel of the large liquid reagent well plate using a central well plate support wall extending from the base of the small liquid reagent well plate receptacle and positioned between a first end wall and a second end wall of the small liquid reagent well plate receptacle.

[0196] In another implementation, supporting a panel of a large liquid reagent well plate includes supporting the panel using a plurality of central well plate support walls of a large liquid reagent well plate receptacle.

[0197] In another implementation, the panel of the large liquid reagent well plate is supported by the central well plate support of the large liquid reagent well plate receptacle, allowing the panel of the large liquid reagent well plate to be substantially flat.

[0198] In another implementation, the coupling between the large liquid reagent well plate and the large liquid reagent well plate receptacle allows the panel of the large liquid reagent well plate to be substantially flat.

[0199] In another implementation, the large liquid reagent well plate includes a reagent well receptacle and a second reagent well receptacle, the second reagent well receptacle having a different size than the reagent well receptacle, and the bulk reagent well is disposed within the second reagent well receptacle.

[0200] In another implementation, the method includes performing a library pooling process in a common bay. In another implementation, the method includes performing at least one of a denaturation process or a dilution process in a common bay.

[0201] In another implementation, a well plate includes rectangular walls including end walls and side walls, the end walls each including a notch and a recess forming a handle extending between the side walls; a panel coupled to the rectangular walls and extending between the rectangular walls, the panel defining a plurality of reagent well receptacles, the panel including a top surface with the end walls and side walls extending outwardly therefrom; and a plurality of reagent wells including ends with annular collars, the reagent wells being positioned within the reagent well receptacles, the annular collars engaging the top surface.

[0202] In another implementation, the method includes removing the lid from the well plate using a gripper at the plate receptacle. In another implementation, removing the lid includes placing a gripper in a lid notch that forms a lid handle extending between the lid sidewalls of the lid and moving the lid away from the well plate.

[0203] In another implementation, the method includes using a gripper to move the well plate from the consumable area to the assay bay. In another implementation, moving the well plate includes placing a gripper in a notch in the well plate that forms a handle for the well plate and moving the well plate away from the consumable area.

[0204] In another implementation, the method includes removing the well plate from the consumable area, which includes removing the well plate from a stack of well plates in the consumable area.

[0205] In another implementation, compressing the gasket includes moving a body of the pipette assembly away from a guide of the pipette assembly and moving a flange of the pipette toward a protrusion of the guide, compressing the gasket.

[0206] In another implementation, moving the body of the pipette assembly away from the guide of the pipette assembly and moving the flange of the pipette towards the protrusion of the guide to compress the gasket includes using a pipette cam assembly.

[0207] In another implementation, the method includes compressing the gasket by moving a body of the pipette assembly away from a guide of the pipette assembly and moving a flange of the pipette toward a protrusion of the guide to engage an inner lobe of a camshaft of a pipette cam assembly of the pipette assembly with a guide bearing of the pipette assembly.

[0208] In another implementation, the method includes relaxing the gasket to allow the pipette tip to be separated from the pipette assembly. In another implementation, loosening the gasket includes moving a body of the pipette assembly toward a guide of the pipette assembly and moving a flange of the pipette away from a protrusion of the guide to loosen the gasket.

[0209] In another implementation, moving the guide of the pipette assembly toward the bar of the pipette assembly and moving the flange of the pipette away from the protrusion of the guide to loosen the gasket includes using a pipette cam assembly.

[0210] In another implementation, the method includes positioning an inner lobe of a camshaft of a pipette cam assembly of the pipette assembly in a second position relative to a guide bearing of the pipette assembly, thereby allowing a flange of the pipette to move away from a protrusion of the guide of the pipette assembly and relaxing a gasket, and allowing the body to move toward the guide of the pipette assembly, allowing the flange of the pipette to move away from the protrusion of the guide and relaxing the gasket.

[0211] In another implementation, a method includes releasing a pipette tip from a pipette assembly. In another implementation, releasing the pipette tip from the pipette assembly includes moving a burr toward a flange of the pipette, engaging the pipette tip with the burr, and biasing the pipette tip to be released from the pipette assembly.

[0212] In another implementation, the method includes using an actuator to move a piston within a barrel of the pipette between a retracted position and an extended position. In another implementation, the method includes performing an amplification process on samples in a well plate disposed on a plate receptacle.

[0213] In another implementation, the method includes performing a cleanup process on samples in a well plate disposed on a plate receptacle. In another implementation, performing the cleanup process includes moving a magnet toward the well plate on the plate receptacle.

[0214] In another implementation, engagement of the cover bearing with the stop wall moves the inner slot bearing within the inner cam slot, moving the cover bearing along the stop wall and moving the cover toward the base to cover the plate receptacle.

[0215] In another implementation, engagement of the cover follower bearing with the rear wall causes the outer slot bearing to move within the outer cam slot, causing the cover follower bearing to move along the rear wall and moving the cover follower toward the base.

[0216] In another implementation, the method includes biasing the cover away from the cover follower. In another implementation, archiving the library of samples includes sealing the samples.

[0217] In another implementation, archiving the library of samples includes freezing the samples. In another implementation, the library pooling process includes preparing an equimolar pool using the samples based on the quantification values ​​determined by the library quantification process.

[0218] In another implementation, the method includes archiving the remainder of the library of samples. In another implementation, archiving the library of samples includes sealing the samples.

[0219] In another implementation, archiving the library of samples includes freezing the samples. In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a library quantification process and a library pooling process on the samples.

[0220] In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a denaturation process on the samples. In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a dilution process on the samples.

[0221] In another implementation, transferring the sequencing-ready sample pool to the sequencer includes transferring the sample library to the sequencing system using a sample shipper assembly.

[0222] In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a library quantification process and a library pooling process on the samples.

[0223] In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a denaturation process on the samples. In another implementation, preparing a sequencing-ready pool of samples in a common bay includes performing a dilution process on the samples.

[0224] Each flow cell port is coupled to a corresponding port of the flow cell interface and associated with one of the multiple channels of the flow cell via a flow cell fluid line.

[0225] In another implementation, the sample valve is movable to fluidly couple a sipper of the library preparation system, a sample port of the sequencing instrument, and a corresponding outlet of one of the multiple channels of the flow cell.

[0226] In another implementation, the sample valve is movable to fluidly decouple a sipper of the library preparation system, a sample port of the sequencing instrument, and a corresponding outlet of one of the multiple channels of the flow cell.

[0227] In another implementation, the sample valve is operable to individually load each channel of a plurality of channels of the flow cell. In another implementation, the sequencing instrument includes a plurality of pumps, and the body of the sample loading assembly defines a plurality of pump ports, each pump port coupled to one of the plurality of pumps. In another embodiment, each sample valve is operable to fluidly couple a sipper of the sample sipper assembly of the library preparation system to a corresponding pump of the plurality of pumps of the sequencing instrument, and to fluidly couple one of the plurality of pumps to a corresponding channel of the plurality of channels of the flow cell.

[0228] In another implementation, the pump is operable to individually control fluid flow in each of the multiple channels of the flow cell. In another implementation, the outlets of the multiple channels are fluidly connectable to a waste reservoir.

[0229] In another implementation, the sequencing instrument includes a pump manifold assembly including a plurality of pumps, the pump manifold assembly fluidly coupling outlets of the plurality of channels to a waste reservoir.

[0230] In another implementation, the sequencing instrument includes a pump manifold assembly including a pump and a cache, The sequencing instrument further includes a bypass valve and a bypass fluid line coupling the bypass valve and the cache.

[0231] In another implementation, the sequencing instrument further comprises a shared line valve, a plurality of dedicated reagent fluid lines, and a shared reagent fluid line, wherein the shared reagent fluid line connects the shared line valve to the central valve and is adapted to flow one or more reagents to the flow cell, and each dedicated reagent fluid line connects the bypass fluid line to the central valve and is adapted to flow one or more reagents toward the flow cell.

[0232] In another implementation, a pump manifold assembly carries a plurality of pump valves and cache valves and includes a plurality of pump channel fluid lines, a plurality of pump fluid lines, a shared fluid line, a cache fluid line, and a main waste fluid line, the cache fluid lines are coupled to the cache and cache valves and between the cache and cache valves, each pump valve is coupled to a corresponding pump channel fluid line, a corresponding pump fluid line, and a shared fluid line, and the cache valves are coupled to the cache fluid line, the main waste fluid line, and the shared fluid line.

[0233] In another implementation, the pump valve and pump are operable to individually control fluid flow in each of the multiple channels of the flow cell, and the pump valve, cache valve, and pump are operable to control fluid flow between a bypass fluid line and a shared fluid line.

[0234] In another implementation, the pump valve, the cache valve, and the pump are operable to control the flow of fluid between the shared fluid line and the main waste line. In another implementation, the sequencing instrument includes a pump manifold assembly having a plurality of pumps including a pump and a plurality of pump valves, each pump and corresponding pump valve operable to individually control the flow of a target sample between each sipper of a sample sipper assembly of the library preparation system and a corresponding channel of the flow cell.

[0235] In another implementation, the sequencing instrument includes a sample loading assembly having a plurality of sample valves, each operable to individually load a sample of interest into each channel of a plurality of channels of a flow cell.

[0236] In another implementation, the device includes a flow cell assembly including a flow cell having a plurality of channels and a flow cell manifold, the flow cell manifold including an inlet, a plurality of fluid lines, and a plurality of outlets, each outlet of the flow cell manifold coupled to a corresponding channel of the flow cell.

[0237] In another implementation, the method includes moving a second sample valve of the one or more sample valves to a first position to fluidically couple a second sipper of a sipper manifold assembly of the library preparation system to a second pump of the sequencing instrument, drawing a second target sample from the library preparation system through the second sipper of the sipper manifold assembly toward the second pump of the sequencing instrument, moving the second sample valve to a second position to fluidically couple the second pump to a second channel of a flow cell coupled to a flow cell interface of the sequencing instrument, and pumping the second target sample into the second channel of the flow cell through an outlet of the second channel.

[0238] In another implementation, the method includes fluidly coupling a reagent reservoir to an inlet of a channel of a flow cell. In another implementation, pumping the first target sample from the first sample reservoir into the channel of the flow cell includes moving the first target sample from a sample cartridge in the library preparation system using a sipper of the sipper manifold assembly, out an associated pump port of the sample loading assembly, to a corresponding sample port of the sample loading assembly of the sequencing instrument, and into a pump channel fluid line of the pump manifold assembly of the sequencing instrument; and moving the first target sample from the pump channel fluid line through the associated pump port and through a corresponding flow cell port of the sample loading assembly, each flow cell port being coupled to a corresponding port of the flow cell interface and associated with one of the channels of the plurality of channels of the flow cell.

[0239] In another implementation, moving a first sample valve of the one or more sample valves to a first position includes fluidically coupling a sample port of a sample loading assembly of the sequencing instrument, a sipper of a sample sipper assembly, and a corresponding pump of the sequencing instrument, and moving the first sample valve of the one or more sample valves to a second position includes fluidically coupling the corresponding pump and a channel of the plurality of channels of the flow cell.

[0240] In another implementation, the method includes operating one or more of a plurality of pumps of a sequencing instrument to individually control fluid flow in each of a plurality of channels of a flow cell.

[0241] In another implementation, the method includes flowing a first sample of interest from a first channel of a flow cell to an auxiliary waste line of a sequencing instrument, the auxiliary waste line being upstream of the flow cell and fluidically coupled to a central valve and a waste reservoir of the sequencing instrument.

[0242] In another implementation, the inlet of the first channel is fluidly connected to the waste reservoir through the central valve when the central valve is in the first position, and the sequencing instrument includes the waste reservoir and the central valve.

[0243] In another implementation, the method includes moving a central valve to a second position to fluidly couple a reagent reservoir with a channel of the flow cell and a second channel, and pumping a first volume of reagent through the first channel into a waste reservoir.

[0244] In another implementation, the method further includes flowing a lag buffer through the channels of the flow cell before the sample of interest. In another implementation, the method includes drawing an air bubble into a fluid line between the read buffer and the sample of interest.

[0245] In another implementation, the method includes drawing an air bubble into a fluid line between the lag buffer and the sample of interest. In another implementation, the method includes flowing a disinfectant through the fluid line.

[0246] In another implementation, the disinfectant includes bleach. In another implementation, the read buffer and the lag buffer comprise a buffer. It is understood that all combinations of the foregoing concepts and additional concepts, described in more detail below (provided such concepts are not mutually inconsistent), are considered to be part of the subject matter disclosed herein and / or can be combined to achieve particular benefits of particular embodiments described herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are considered to be part of the subject matter disclosed herein. [Brief explanation of the drawings]

[0247] [Figure 1-1] 1 shows a schematic diagram of one implementation of a system according to the teachings of the present disclosure. [Figure 1-2]1 shows a schematic diagram of one implementation of a system according to the teachings of the present disclosure. [Figure 2] FIG. 2 is a schematic diagram illustrating one implementation of another system that can be used to implement the system of FIG. 1. [Figure 3] FIG. 2 is an isometric view of another system implementation that can be used to implement the system of FIG. 1. [Figure 4] FIG. 4 is a detailed isometric view of the system of FIG. 3 showing the lid removed from one of the work areas and the lid shown in another one of the work areas. [Figure 5] FIG. 4 is another detailed isometric view of the system of FIG. 3. [Figure 6] 4 is another detailed isometric view of the system of FIG. 3 showing the first work area, actuator, lid, and contact dispenser. [Figure 7] FIG. 4 is another detailed isometric view of the system of FIG. 3 showing two of the first work areas and two of the contact dispensers. [Figure 8] FIG. 4 is a detailed isometric view of the system of FIG. 3 showing a first work area and a first plate receptacle. [Figure 9] FIG. 4 is a detailed isometric view of the system of FIG. 3 showing the second work area and a portion of one of the first work areas. [Figure 10] 4 is a detailed isometric view of the system of FIG. 3 showing a loading area including a shipper assembly and a stage that moves a plate receptacle relative to the shipper assembly. [Figure 11] FIG. 4 is a detailed isometric view of the system of FIG. 3 showing the loading area including the shipper assembly with the shipper assembly housing removed to show the shipper. [Figure 12] FIG. 2 is a front view of another implementation of a system that can be used to implement the system of FIG. 1. [Figure 13] FIG. 13 is a top view of the system of FIG. 12. [Figure 14] FIG. 13 is an isometric view of one of the consumable areas and one of the first work areas of the system of FIG. 12. [Figure 15] FIG. 1 is an isometric view of one of the consumable areas serviced by the drawer shown in the extended position. [Figure 16] 13 is a top view of one of the consumable areas and one of the first work areas of the system of FIG. 12. FIG. [Figure 17] FIG. 13 is a top view of one of the consumable areas of the system of FIG. 12. [Figure 18] FIG. 13 is an isometric view of the contact dispenser, mover, and stage of the system of FIG. 12. [Figure 19] FIG. 13 is a top view of the second work area and loading area of ​​the system of FIG. 12. [Figure 20] 2 is an isometric view of an implementation of another system that can be used to implement the imaging system of FIG. 1. [Figure 21] FIG. 21 is a detailed isometric view of the consumable area, first work area, and second work area of ​​the system of FIG. 20. [Figure 22] FIG. 21 is a detailed isometric view of the consumable area, first work area, second work area, and loading area of ​​the system of FIG. 20. [Figure 23] FIG. 1 is a schematic diagram illustrating an implementation of another system in accordance with the teachings of the present disclosure. [Figure 24A-1] FIG. 1 is a schematic diagram illustrating an implementation of another system in accordance with the teachings of the present disclosure. [Figure 24A-2] FIG. 1 is a schematic diagram illustrating an implementation of another system in accordance with the teachings of the present disclosure. [Figure 24B] FIG. 24B is a schematic diagram illustrating one implementation of a portion of a pump manifold assembly for use with the system of FIG. 24A. [Figure 24C] FIG. 1 illustrates the process of loading one or more samples of interest from a library preparation system and loading these samples of interest into a flow cell of a sequencing instrument. [Figure 24D] FIG. 1 illustrates the process of loading one or more samples of interest from a library preparation system and loading these samples of interest into a flow cell of a sequencing instrument. [Figure 24E] FIG. 1 illustrates the process of loading one or more samples of interest from a library preparation system and loading these samples of interest into a flow cell of a sequencing instrument. [Figure 24F] FIG. 1 illustrates the process of loading one or more samples of interest from a library preparation system and loading these samples of interest into a flow cell of a sequencing instrument. [Figure 25] 1 is a schematic diagram illustrating an implementation of a shipper assembly of a first system and a second system carrying multiple flow cells. [Figure 26] FIG. 2 is a schematic diagram illustrating one implementation of another system that can be used to implement the system of FIG. 1. [Figure 27] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 28] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 29] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 30-1] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 30-2] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 30-3] FIG. 1 illustrates a workflow that can be performed using the teachings of the present disclosure. [Figure 31] 1 is a schematic diagram illustrating an implementation of a shipper assembly of a first system and a second system carrying multiple flow cells. [Figure 32] FIG. 2 illustrates an implementation of another system that can be used to implement the system of FIG. 1. [Figure 33] FIG. 33 is a plan view of the system of FIG. 32. [Figure 34] FIG. 33 is a front view of the system of FIG. 32. [Figure 35]FIG. 33 is an isometric view of one of the assay bays of the system 3300 of FIG. 32. [Figure 36] A top view of the assay bay of Figure 35, including a pipette assembly, thermocycler, magnet, and drawer used to perform the amplification and cleanup processes associated with preparing a library of samples for sequencing. [Figure 37] FIG. 37 is an isometric view of a portion of the exemplary pipette assembly of FIG. 36. [Figure 38] FIG. 38 is an isometric view of the pipette assembly of FIG. 37 with guide 3348 removed. [Figure 39] FIG. 39 is a front cross-sectional view of the pipette assembly of FIG. 38. [Figure 40] FIG. 39 is a rear cross-sectional view of the pipette assembly of FIG. 38. [Figure 41] FIG. 39 is a front view of the pipette assembly of FIG. 38, including the printed circuit board assembly. [Figure 42] FIG. 39 is a side view of the pipette assembly of FIG. 38 showing the end of the pipette inserted into the pipette tip. [Figure 43] 43 is a side view of the pipette assembly of FIG. 38, showing the camshaft rotated 90° relative to the position of the camshaft in FIG. 42. [Figure 44] 44 is a side view of the pipette assembly of FIG. 38, showing the camshaft rotated 90° relative to the position of the camshaft in FIG. 43. [Figure 45] 45 is a side view of the pipette assembly of FIG. 38, showing the camshaft rotated 90° relative to the position of the camshaft in FIG. 44. [Figure 46] FIG. 33 is an isometric view of one thermocycler of the assay bay of FIG. 32. [Figure 47] FIG. 47 is an enlarged isometric view of the thermocycler of FIG. 46. [Figure 48] FIG. 47 is an isometric view of the thermocycler of FIG. 46, with the inner cam plate, outer cam plate, sled, and spring omitted. [Figure 49]FIG. 1 is a side view of the thermocycler with the cover assembly in the rear position and not covering the plates. [Figure 50] FIG. 1 is a side view of the thermocycler with the cover assembly in a forward, lowered position covering the plates. [Figure 51] FIG. 33 is an isometric view of one drawer of the assay bay of FIG. 32. [Figure 52] FIG. 52 is an isometric view of the drawer of FIG. 51 with the consumables removed but including the dry well plate receptacle and waste reservoir. [Figure 53] FIG. 52 is an isometric view of the drawer of FIG. 51 with the consumable and dry well plate receptacles removed. [Figure 54] FIG. 52 is a top view of the drawer of FIG. 51, including consumables, a dry well plate receptacle, and a waste reservoir. [Figure 55] FIG. 52 is a side view of the drawer of FIG. 51, including consumables, a dry well plate receptacle, and a waste reservoir. [Figure 56] 33 is an isometric view of a reagent well plate including a first end wall, a second end wall, and a panel that can be used with the system of FIG. 32. [Figure 57] FIG. 57 is a side view of the reagent well plate of FIG. 56. [Figure 58] FIG. 57 is an isometric view of one of the reagent wells of the reagent well plate of FIG. 56. [Figure 59] FIG. 10 is an isometric view of another reagent well plate including a first end wall, a second end wall, and a panel. [Figure 60] FIG. 60 is a side view of the reagent well plate of FIG. 59. [Figure 61] FIG. 61 is a side view of the bulk reagent well of FIG. 60. [Figure 62] FIG. 61 is an isometric view of the bulk reagent well of FIG. 60. [Figure 63] 33 is an isometric view of another reagent well plate including a first end wall, a second end wall, and a panel that can be used with the system of FIG. 32. [Figure 64] FIG. 64 is a side view of the reagent well plate of FIG. 63. [Figure 65] FIG. 64 is an isometric view of a reagent well of the reagent well plate of FIG. 63. [Figure 66] FIG. 33 is an isometric view of a well plate that can be used with the system of FIG. 32. [Figure 67] FIG. 67 is an isometric view of the stack of well plates of FIG. 66. [Figure 68] FIG. 67 is a cross-sectional end view of the stack of well plates of FIG. 66. [Figure 69] FIG. 67 is a top view of the well plate of FIG. 66. [Figure 70] FIG. 67 is a side view of the well plate of FIG. 66. [Figure 71] FIG. 33 is an isometric view of another stack of well plates that can be used with the system of FIG. 32. [Figure 72] FIG. 72 is a bottom isometric view of the well plate of FIG. 71. [Figure 73] FIG. 72 is a cross-sectional end view of the stack of well plates of FIG. 71. [Figure 74] FIG. 67 is an isometric view of a stack of lids that can be used to cover the well plate of FIG. 66. [Figure 75] FIG. 72 is an isometric view of a lid that can be used to cover the well plate of FIG. 71. [Figure 76] FIG. 1 is a top view of an exemplary sample cartridge including multiple wells that can be used with any of the disclosed implementations. [Figure 77] FIG. 1 is a top view of an exemplary reagent cartridge including multiple wells that can be used with any of the disclosed implementations. [Figure 78-1] FIG. 2 is a plan view of an exemplary system that can be used to implement the system of FIG. 1. [Figure 78-2] FIG. 2 is a plan view of an exemplary system that can be used to implement the system of FIG. 1. [Figure 79] FIG. 79 is a front isometric view of one implementation of the system of FIG. 78. [Figure 80] FIG. 79 is a rear isometric view of one implementation of the system of FIG. 78. [Figure 81] FIG. 80 is an isometric view of one of the assay bays of the system 5050 of FIG. 79. [Figure 82] FIG. 82 is an isometric view of the assay bay of FIG. 81 with the drawer partially removed. [Figure 83] 33 is an isometric view of one exemplary implementation of an assay bay including an alternative pipette assembly that can be used to implement the system of FIG. 1 and / or the system of FIG. 32. [Figure 84] FIG. 84 is a side view of the assay bay drawer of FIG. 83. [Figure 85] FIG. 2 is a plan view of an exemplary system that can be used to implement the system of FIG. 1. DETAILED DESCRIPTION OF THE INVENTION

[0248] Although the following text discloses detailed descriptions of implementations of methods, apparatus, and / or products, it should be understood that the legal scope of ownership is defined by the claims at the end of this patent. Accordingly, the following "Detailed Description" should be construed as exemplary only and does not describe every possible implementation, as describing every possible implementation would be impractical, if not impossible. Numerous alternative implementations may be implemented using either current technology or technology developed after the filing date of this patent. It is contemplated that such alternative implementations would still fall within the scope of the claims.

[0249] At least one aspect of the present disclosure relates to a system that automates the library preparation process and uses fewer consumables, thereby reducing the system's footprint and the amount of solid waste generated. The disclosed system also uses a single well plate for many operations, resulting in a smaller workload / reagent volume. The system stores consumables and reagents for multiple runs, allowing for variable batch processing, allowing a single sample to be processed without consuming the reagents associated with, for example, a 24-sample kit.

[0250] The disclosed implementations enable workflows from extracted materials through library preparation and / or the ability to automate assays of varying complexity. The disclosed implementations enable the ability to run multiple assay workflows in parallel and / or perform staggered starts. The disclosed implementations enable the ability to run variable batch sizes and / or provide easy consumable loading with low touchpoints. The disclosed implementations enable architecture scalability (e.g., 24, 48 samples), on-board library quantification, and / or on-board library pooling, denaturation, and / or dilution. The disclosed implementations enable the ability to transfer libraries to a sequencer and / or manage cross-contamination. The disclosed implementations, by way of example, enable minimizing plastic waste and / or minimizing increases in cost per sample relative to manual library preparation workflows. The disclosed implementations enable no or only a small increase in assay runtime relative to manual library preparation workflows and / or enable no or only limited changes in assay performance relative to manual library preparation workflows. The disclosed implementations enable high sample success rates and / or instrument uptime and / or provide a small instrument footprint. The disclosed implementations enable digital systems integration (e.g., LIMS) and / or operate in a standard laboratory.

[0251] The disclosed implementations allow for the integration of extraction and / or integration with a sequencer. The disclosed implementations allow for architectural scalability (e.g., 96 samples) and / or provide multiple "assay bays" and a single "common bay." Any number of "assay bays" (e.g., 12 assay bays) can be included. In one example, the disclosed implementations allow for assay automation of greater than about 90% within an individual assay bay. However, other percentages of assay automation up to about 90% may be achieved within an individual assay bay. In one example, the disclosed implementations allow for up to 12 samples to be processed within each assay bay. However, the disclosed implementations can process more or fewer samples than 12 samples. The disclosed implementations allow for systems configured as two assay bays (24 samples), four assay bays (48 samples), etc., although other bay counts may be used. The disclosed implementations allow for the common bay to be utilized to quantify, pool, denature, and / or dilute samples from multiple assay bays. In one example, the disclosed implementations allow different assays to be run in parallel in different assay bays. The disclosed implementations allow assay bays to be accessed and / or started at different times (staggered starts). The disclosed implementations allow integrated thermal magnet stations in each assay bay to reduce footprint and increase workflow control. The disclosed implementations use pipette mixing in some examples and do not include a shaker. The assay bays and / or common bay may include a reagent cooler in some implementations.

[0252] 1 shows a schematic diagram of one implementation of a system 300 according to the teachings of the present disclosure. The system 300 can be used, for example, to automatically, easily, and efficiently prepare DNA libraries for sequencing applications. The system 300 includes a consumable area 302, a first work area 304, a second work area 306, and a loading area 308. The second work area 306 also includes a consumable area 309 in the illustrated implementation. The consumable area 302 and the first work area 304 may be referred to as first bays (e.g., first assay bays), and the second work area 306 may be referred to as a common bay. The system 300 may include any number of consumable areas 302 and a corresponding number of first work areas 304. The system 300 may include four consumable areas 302 and four first work areas 304, as shown in FIGS. 2-4, or the system 300 may include two consumable areas 302 and two first work areas 304, as shown, for example, in FIGS. 20 and / or 32. Other numbers of work areas may be used. When more than one consumable area 302 / first work area 304 is included, the system 300 may execute a corresponding number of workflows simultaneously and / or at different times. As an example, one workflow (e.g., one assay) may be executed in one of the first work areas 304, and another workflow (e.g., a second assay) may be executed in another one of the first work areas 304.

[0253] In some implementations, the system 300 may perform a DNA library preparation workflow, including an amplification process, a cleanup process, a quantification process, a library normalization process, a pooling process, a denaturation process, and / or a dilution process. The loading area 308 may be associated with loading and / or transporting prepared samples to a system, such as a sequencing system and / or a next-generation sequencing system (see FIG. 24A). The first work area 304 may be associated with the amplification and cleanup processes, and the second work area 306 may be associated with the quantification process, the library normalization process, the pooling process, the denaturation process, and / or the dilution process.

[0254] System 300 can execute different workflows. The workflows can include, by way of example, a whole genome sequencing (WGS) workflow, a DNA and RNA enrichment workflow, a methylation workflow, a split-pool amplicon workflow, an amplicon workflow, an exome sequencing workflow, a ChIP-seq workflow, a methyl-seq workflow, a metagenomics workflow, a mate pair workflow, a single cell workflow, a cDNA workflow, a ligation workflow, an adapter ligation workflow, a tagmentation workflow, a multiplexing workflow, and / or a long-read workflow. DNA library preparation workflows can be performed on any number of samples (e.g., from 1 to 24 samples). Thus, system 300 allows for variable batch processing.

[0255] Consumable areas 302 and / or 309 can be used to load and store reagents and consumables required for library preparation. Processes include disposable tips, wet or dry assay-specific reagents, wet or dry bulk reagents, and reaction plates and wells. Consumable area 302 includes consumable receptacle 310, which is shown to receive tip tray 114 having first and second tips 116 and 118, first plate 120 having wells 122 containing samples 124, and second plate 126 having wells 128. Consumable receptacle 310 may be a drawer that can be withdrawn from system 300 and loaded with consumables 114, 116, 118, 120, and 126. Consumable receptacle 310 is also shown with lid 130, index tray 132 having wells 134 containing indexes 136, bead tray 138 having wells 140 containing beads 141, liquid reservoir 312, and dry reagent reservoir 314. One or more of these reagents 136 and / or 141 may be lyophilized and included with dry reagent reservoir 314. Second work area 306 may also have tip tray 114 and third plate 142 having wells 143.

[0256] The first plate 120, the second plate 126, the third plate 142, the index tray 132, and / or the bead tray 138 may be stacks of corresponding plates 120 and / or 126 and / or trays 132 and / or 138. The first plate 120, the second plate 126, and the third plate 142 may be stacked in some implementations, while the index tray 132 and / or the bead tray 138 may not be stacked. Other approaches may also prove suitable. The chip tray 114 may have a plurality of first chips 116, a plurality of second chips 118, and / or one or more chips of a different size than the first chips 116 and / or the second chips 118. The chips in the chip tray 114 may be reusable for at least multiple portions of a workflow, as described in more detail below. Although chip tray 114 is described as having first chip 116 and second chip 118, chip tray 114 can have any number of chips, such as 24 chips. However, plates 120, 126, 142 may have any number of wells.

[0257] Although plates 120 and 126 are described as having a single well 122, 128, plates 120, 126 may have multiple wells, such as 24 wells. Plates 120, 126, in some implementations, may include a 2×12 array of wells, allowing side access to all wells. Plates 120, 126 implemented with a 2×12 array allow loading levels / air bubbles to be inspected in all wells using side-view computer vision, increasing the chance of heat transfer in heating (PCR) operations and magnetic pull-down operations.

[0258] The system 300 includes a mover 144, and a first work area 304 includes a contact dispenser 145, a stage 148, a magnet 150, and a thermocycler 152. A contact dispenser 318 may, in some implementations, be included in the first work area 304. The contact dispenser 145 may be movable to aspirate / dispense liquid into the consumable area 302 and / or the first work area 304.

[0259] Stage 148 may be an xz stage, such that stage 148 is movable in the x and z directions (but not in the y direction). Stage 148 and contact dispenser 145 may, as a result, be movable to aspirate and / or dispense fluid between and above consumable area 302 and first working area 304. Contact dispenser 145 may, for example, be movable linearly in the x direction, thereby reducing the risk of cross-contamination (between different samples) and allowing some or all of the tips used in system 300 to be reusable for at least some of the processes performed by system 300. However, stage 148 may be implemented differently.

[0260] The second work area 306 includes the analyzer area 154, and the system 300 also includes, in the illustrated implementation, a contact dispenser 318 and a stage 320. The stage 320 may be referred to as a cross-bay gantry. The contact dispenser 318 may additionally or alternatively be implemented with a non-contact dispenser for aspirating / dispensing throughout the system 300. The dispenser 318 and the stage 320 may operate in the first work area 304 and the second work area 306.

[0261] The contact dispenser 318 may be movable to aspirate / dispense liquid into the consumable area 302, the first work area 304, and / or the second work area 306. In some implementations, the contact dispenser 318 may carry two tips (or two sets of tips), one of the tips capable of holding a first volume of fluid and the other of the tips capable of holding a second volume of fluid. The contact dispenser 318 may include two contact dispensers, each carrying one of the tips. The two contact dispensers may be movable independently relative to each other. The first volume may be approximately 50 microliters, and the second volume may be approximately 500 microliters.

[0262] The stage 320 may be an xyz stage, and the mover 144 may be movable in the x, y, and z directions. As a result, the stage 320 and the contact dispenser 318 may be movable to aspirate and / or dispense fluid between and above the consumable area 302, the first working area 304, and / or the second working area 306.

[0263] The mover 144 can include a robotic arm and / or can include a gripper. The stage 320 can carry the mover 144 and the contact dispenser 318 in some implementations.

[0264] The second work area 306 may also include a light bar 155 that may be used to degrade oligonucleotides. In some implementations, the first work area 304 may additionally or alternatively include a light bar 155. The light bar 155 may, in some implementations, be a high-power ultraviolet (UV) light bar that is used periodically throughout the workflow to repeatedly degrade oligonucleotides and prevent cross-contamination.

[0265] The first work area 304 includes a first plate receptacle 156 and a second plate receptacle 158, the second work area 306 includes a third plate receptacle 159, a fourth plate receptacle 160, and a fifth plate receptacle 161, and the analyzer area 154 includes a substrate 162 and an imaging system 164 in the illustrated implementation. However, the analyzer area 154 may be implemented differently to perform a quantification process in other implementations. For example, the analyzer area 154 may be a substrate 162 realized by a well plate into which a portion of a sample and a dye are dispensed. The imaging system 164 can image the portion of the sample in the well plate to determine the concentration of the sample.

[0266] The first plate receptacle 156 may include a heat block defining a well receptacle, and the thermocycler 152 may be disposed below the well receptacle. The thermocycler 152 may, in some embodiments, be disposed below the first plate receptacle 156. A heat sink 153 is shown coupled to the thermocycler 152. However, the heat sink 153 may be omitted.

[0267] Plate receptacles 156, 158, 159, 160, and 161 may be referred to as plate stations. Imaging system 164 may be a fluorescence imaging system, i.e., a fluorescence spectrophotometer including an objective lens and / or a solid-state imaging device. The solid-state imaging device may include a charge-coupled device (CCD) and / or a complementary metal-oxide semiconductor (CMOS). Although five plate receptacles 156, 158, 159, 160, and 161 are shown, any number of plate receptacles (e.g., six plate receptacles) may be included.

[0268] The second work area 306 also includes a reagent receptacle 250 having an access opening 252. A reagent reservoir 254 is shown received within the reagent receptacle 250. The first work area 304 may additionally or alternatively include a reagent receptacle 250 having an access opening 252. The reagent receptacle 250 may be refrigerated and may be a drawer that can be withdrawn from the system 300 and loaded with the reagent reservoir 254. The reagent reservoir 254 may be accessed through the access opening 252, for example, by a contact dispenser 318 to aspirate a reagent from the reagent reservoir 254.

[0269] The loading area 308 includes a sipper assembly 174 in the illustrated embodiment. The sipper assembly 174 may be referred to as a sample sipper manifold assembly or a sample sipper assembly. The sipper assembly 174 may include sipper 184. Any number of sipper 184 may be included, such as between two and sixteen sipper 184, by way of example. The sipper assembly 174 may be coupled to a corresponding number of flow cells of another system (e.g., see FIG. 24A ) via the sipper 184. In some implementations, the sipper assembly 174 includes multiple ports, and each port of the sipper assembly 174 may receive one of the sipper 184. The sipper 184 may be referred to as a fluid line. The sipper assembly 174 includes a valve 186 that can be selectively actuated to control the flow of fluid through the fluid line 188. The fluid line 188 may be referred to as a sample sipper assembly. The sipper assembly 174 also includes a pump 187 for selectively flowing the prepared sample from the wells 128, 143 through the sipper 184, through a fluid line 188, and from the system 300 to another system (see, e.g., FIG. 24A). Other systems can be used to perform analysis on one or more target samples. The sample may include one or more DNA clusters that are linearized to form single-stranded DNA (sstDNA). The other systems can be, by way of example, sequencing systems and / or next-generation sequencing systems.

[0270] Valve 186 may be implemented by a rotary valve, a pinch valve, a flat valve, a solenoid valve, a check valve, a piezoelectric valve, or the like. Other fluid control devices may prove suitable. Pump 187 may be implemented by a syringe pump, a peristaltic pump, and / or a diaphragm pump. However, other types of fluid transfer devices may be used. Controller 176 is electrically and / or communicatively coupled to the components of system 300 to perform the various functions disclosed herein. Alternatively, sipper assembly 174 may be omitted.

[0271] The actuator 166 can move the magnet 150 between an upper position, in which the magnet 150 affects any plates placed on the first plate receptacle 156, and a lower position, in which the magnet 150 does not affect any plates placed on the first plate receptacle 156. Moving the magnet 150 relative to the first plate receptacle 156 and any plates 120, 126, 142 placed on the first plate receptacle 156 allows for a smaller area on the first working area 304 to be consumed. The magnet 150 can also move one of the sample-loaded plates 120, 126, 142 with a relatively high degree of reliability compared to alternative approaches that move the sample-loaded plates 120, 126, 142 to a separate magnet station. The magnet 150 can be implemented with a Halbach array configuration to strengthen and focus the corresponding magnetic field.

[0272] The mover 144 moves the first plate 120 from the consumable area 302 to the first plate receptacle 156. Different wells 122 of the first plate 120 may contain different samples 124. The samples 124 may be biological samples of human, animal, plant, bacterial, viral, or fungal origin. Other sources of biological samples may prove suitable. The mover 144 may include a gantry with grippers that can pick up and place objects, such as plates 120, 126 and / or trays 132, 138, between different areas 302, 304, 306, 308 of the system 300. However, the mover 144 may be implemented differently.

[0273] The stage 148 aligns the contact dispenser 145 with the tip tray 114, and the contact dispenser 145 couples with a first tip 116 from the tip tray 114. Although the contact dispenser 145 is described as coupling with one first tip 116, the contact dispenser 145 may couple with a number of first tips 116 corresponding to the number of wells 122 in the first plate 120 and / or the number of wells 122 in the first plate 120 that contain samples 124. For example, the first tip 116 may be a smaller pipette tip used to transfer smaller fluid volumes, and the second tip 118 may be a larger pipette tip used to transfer larger fluid volumes. Each of the first tip 116 and / or second tip 118 may be exposed to only a single sample during a workflow, reducing the possibility of cross-contamination and the need to obtain new tips after each operation. In some library preparation workflows, for example, each of the first tip 116 and / or the second tip 118 may be used throughout the workflow, and the contact dispenser 145 may be coupled to and / or use different ones of the tips 116, 118 depending on the workflow that the system 300 is implementing and / or depending on the processes within the workflow.

[0274] In one example workflow, the stage 148 aligns the contact dispenser 145 with the index tray 132, and the contact dispenser 145 uses the first tip 116 to aspirate the index 136 from the index tray 132. The stage 148 can then align the contact dispenser 145 with the first plate 120, and the contact dispenser 145 dispenses the index 136 into the wells 122 of the first plate 120. The mover 144 moves the lid 130 from the consumable area 302 and places the lid 130 on the first plate 120, covering the wells 122 of the first plate 120. The first work area 304 also includes a lid 322 and an actuator 324. The lid 322 may also be referred to as a cover and / or a door. The actuator 324, when operated, can move the lid 322 relative to the plate receptacle 156 to cover the plate receptacle 156, for example, during an amplification process. Thus, the lid 322 can be positioned to surround the first plate 120 during the amplification process. The lid 130 and / or the lid 322 can surround the first plate 120 during the amplification process.

[0275] The thermocycler 152 is aligned with the first plate receptacle 156, and the thermocycler 152 amplifies the samples 124 in the wells 122 of the first plate 120. In the illustrated implementation, the thermocycler 152 and / or the magnet 150 can act on the plates 120, 126 received in the first plate receptacle 156. Alternatively, the thermocycler 152 can be positioned remotely from the magnet 150.

[0276] After the amplification process is complete, the actuator 324 can move the lid 322 away from the first plate 120, and / or the mover 144 can move the lid 130 from the first plate 120 to the consumable area 302. The thermocycler 152 may include the lid 322 that covers the first plate 120, or a separate consumable lid may be positioned on top of the first plate 120, for example, between the first plate 120 and the lid 322. The consumable area 302 includes a waste 192 that can receive used consumables, such as the lid 130. However, alternatively, the lid 130 may be reused. The waste 192 may be a waste tray having an absorbent material that absorbs liquid waste.

[0277] The system 300 can perform a cleanup process after the amplification process is performed. The stage 148 aligns the contact dispenser 145 with the bead tray 138, and the contact dispenser 145 aspirates the beads 141 from the bead tray 138. The contact dispenser 145 may aspirate the beads 141 using the same first tip 116 used to aspirate the index 136. Alternatively, the contact dispenser 145 may use another one of the first tips 116 or one of the second tips 118 to aspirate the beads 141.

[0278] Stage 148 aligns contact dispenser 145 with first plate 120, and contact dispenser 145 dispenses beads 141 into wells 140 of first plate 120 as part of the clean-up process. Stage 148 aligns contact dispenser 145 with liquid reservoir 312, and contact dispenser 145 aspirates first reagent 194 from liquid reservoir 312. Stage 148 then aligns contact dispenser 145 with first plate 120, and contact dispenser 145 dispenses first reagent 194 into wells 122 of first plate 120. Alternatively, the contact dispenser 145 may aspirate the hydrating liquid 195 from the liquid reservoir 312 and then dispense the hydrating liquid 195 into the dry reagent 197 contained in the dry reagent reservoir 314 to rehydrate the dry reagent 197 and form the first reagent 194. The contact dispenser 145 may pipette mix the dry reagent 197 and the hydrating liquid 195. The first reagent 194 may be a bead buffer, and the sample 124 may bind to the beads 141 in the presence of the bead buffer. In some implementations, the contact dispenser 145 may be capable of jet dispensing at a liquid velocity appropriate to enable jet mixing. The system 300 may also include a shaker to enable mixing.

[0279] The stage 148 aligns the contact dispenser 145 with the tip tray 114, the contact dispenser 145 places a first tip 116 into the tip tray 116, and then the contact dispenser 145 mates with a second tip 118 from the tip tray 114. Although the contact dispenser 145 is described as mateable with one second tip 118, the contact dispenser 145 may mate with a number of second tips 118 corresponding to the number of wells 122 in the first plate 120 and / or the number of wells 122 in the first plate 120 that contain samples 124.

[0280] Actuator 166 moves magnet 150 toward plate receptacle 156, and magnet 150 attracts beads 141 toward magnet 150. Beads 141 and samples 124 bound to beads 141 can be positioned toward the bottom of wells 122 of first plate 120 or on the sides of wells 122. Chips 116 and / or 118 can easily access wells 122 when beads 141 are on the sides of wells 122. However, magnet 150 can position beads 141 anywhere within wells 122.

[0281] Stage 148 aligns contact dispenser 145 with first plate 120, and contact dispenser 145 aspirates first reagent 194 from wells 122 of first plate 120. Contact dispenser 145 may dispense first reagent 194 aspirated from wells 122 of first plate 120 into waste 192.

[0282] Stage 148 aligns contact dispenser 145 with liquid reservoir 312, contact dispenser 145 aspirates second reagent 198 from liquid reservoir 312, stage 148 then aligns contact dispenser 145 with first plate 120, contact dispenser 145 dispenses second reagent 198 into wells 122 of first plate 120. Alternatively, contact dispenser 145 may aspirate hydrating liquid 195 from liquid reservoir 312 and then dispense hydrating liquid 195 into dry reagent 199 contained within dry reagent reservoir 314 to rehydrate dry reagent 199 and form second reagent 198. The second reagent 198 may be an elution buffer that releases the sample 124 from its binding to the beads 141, and in particular, releases the DNA associated with the sample 124 from its binding to the beads 141.

[0283] The mover 144 moves the second plate 126 from the consumable area 302 to the second plate receptacle 158. The system 300 can use the second plate 126 for the transfer operation. Alternatively, the second plate 126 can remain in the consumable area 302 during the transfer operation. The actuator 166 moves the magnet 150 toward the second plate receptacle 158, attracting the beads 141 toward the magnet 150 and thus providing an eluate into the well 122 that contains the second reagent 198 and the sample 124 but is substantially free of beads.

[0284] The stage 148 aligns the contact dispenser 145 with the first plate 120, and the contact dispenser 145 aspirates the second reagent 198 and the sample 124 from the wells 122 of the first plate 120, for example, using the second tip 118. The stage 148 aligns the contact dispenser 145 with the second plate 126, and the contact dispenser 145 dispenses the second reagent 198 and the sample 124 into the wells 128 of the second plate 126. Alternatively, the second plate 126 may be placed in the consumable area 302 as the contact dispenser 145 dispenses the second reagent 198 and the sample 124 into the wells 128 of the second plate 126. In such an implementation, the second plate receptacle 158 may be omitted from the second work area 306.

[0285] The system 300 may perform a quantification process after the cleanup process is performed. In some implementations, the mover 144 moves the second plate 126 from the first work area 304 to the plate receptacle 159 in the second work area 306 to begin the quantification process. Alternatively, the mover 144 may move the second plate 126 from the consumable area 302 to the plate receptacle 159 in the second work area 306 to begin the quantification process while the second plate 126 remains in the consumable area 302 during the transfer operation. In some implementations, the stage 320 aligns the contact dispenser 318 with the tip tray 114 in the second work area 306, and the contact dispenser 145 couples with tips 326 from the tip tray 114.

[0286] The substrate 162 may be a plate having wells. The substrate may be a consumable item that is disposed of after use. The imaging system 164 may be spaced apart from the substrate 162 and coupled to a portion of the system 300, such as a frame of the system 300. Alternatively, the imaging system 164 may be carried by a stage.

[0287] To perform the quantification process, stage 320 aligns contact dispenser 318 with second plate 126, and contact dispenser 318 aspirates second reagent 198 and a portion of sample 124 from well 128 of second plate 126. The second reagent 198 and a portion of sample 124 may be approximately 2 μL.

[0288] The stage 320 aligns the contact dispenser 318 with the substrate 162, and the contact dispenser 318 dispenses, by way of example, a second reagent 198 and a portion of the sample 124 into the wells of the substrate 162. A dye may also be dispensed into the wells of the substrate 162 by the contact dispenser 318. The imaging system 164 acquires image data of the second reagent 198 and the portion of the sample 124 in the wells of the substrate 162. The imaging system 164 and / or the system 300 use the image data to determine the concentration of the sample 124. The mover 144 can move the substrate 162 to the waste 192 in the consumables area 309 of the second work area 306.

[0289] Alternatively, the substrate 162 may be implemented by a pair of plates 200, 202 defining a gap 204 therebetween. In such implementations, the substrate 162 includes an inlet 206 and an outlet 208 in fluid communication with the gap 204, and a seal 210 disposed between the pair of plates 200, 202. The plates 200, 202 and the seal 210 define a channel 212 between the inlet 206 and the outlet 208. A waste reservoir 214 may be fluidly coupled to the outlet 208 of the substrate 162 by a fluid line 216.

[0290] In an alternative implementation of the substrate 162, the stage 320 aligns the contact dispenser 318 with the inlet 206 of the substrate 162, and the contact dispenser 318 dispenses the second reagent 198 and a portion of the sample 124 into the inlet 206 of the substrate 162. In this embodiment, the second reagent 198 and the portion of the sample 124 may flow and / or be disposed between the inlet 206 and the outlet 208, and the imaging system 164 acquires image data of the second reagent 198 and the portion of the sample 124. The imaging system 164 and / or the system 300 use the image data to determine the concentration of the sample 124. Negative pressure, oil, and / or another substance may be used to bias the second reagent 198 and the portion of the sample 124 between the inlet 206 and the outlet 208. Alternatively, the first plate 200 may be hingedly or removably coupled to the second plate 202 before the first plate 200 is placed on the second plate 202 to allow the contact dispenser 318 to dispense the second reagent 198 and a portion of the sample 124 onto the second plate 202. However, the system 300 may perform the quantification process differently.

[0291] The system 300 may perform a normalization process after the quantification process is performed. In some implementations, the stage 320 aligns the contact dispenser 318 to begin the normalization process. The contact dispenser 318 aspirates a diluent 330 from a liquid reservoir 331 in the second work area 306. The stage 320 then aligns the contact dispenser 318 with the second plate 126, and the contact dispenser 318 dispenses the diluent 330 into the wells 128 of the second plate 126 to dilute the sample 124 based on the determined sample concentration. The sample 124 in the wells 128 of the second plate 126 will have a concentration within the threshold after the diluent 330 is added to the wells 128. The diluent 330 may be a buffer.

[0292] The system 300 may perform a pooling process after the quantification process is performed. In some implementations, the stage 320 aligns the contact dispenser 318 with the tip tray 114 of the second work area 306, the contact dispenser 318 places a tip 326 into the tip tray 114, and the contact dispenser 318 then combines with another tip 328 from the tip tray 114 to begin the pooling process. The mover 144 moves the plate 142 from the second work area 306 to the plate receptacle 160 of the second work area 306. The stage 320 aligns the contact dispenser 318 with the second plate 126, and the contact dispenser 318 aspirates the sample 124 from the wells 128 of the second plate 126. The stage 320 then aligns the contact dispenser 318 with the third plate 142, and the contact dispenser 318 dispenses the sample 124 into the well 143 of the third plate 142. Additional samples from other wells of the second plate 126 can be deposited into the wells 143 of the third plate 142 in a similar manner to combine multiple normalized samples together. A single tip can be used for the pooling process. The contact dispenser 318 can pipette directly from the final archive library wells into the pool, thus allowing one tip per sample to be used.

[0293] The system 300 may perform a denaturation process after the pooling process is performed (although in some implementations, denaturation need not be performed). In some implementations, the stage 320 aligns the contact dispenser 318 with the tip tray 114 of the second work area 306, the contact dispenser 318 places a tip 328 into the tip tray 114, and the contact dispenser 318 then couples with another tip 333 from the tip tray 114 to begin the denaturation process. However, in some implementations, the contact dispenser 1318 may use the same tip 328 used during the pooling process. The stage 320 aligns the contact dispenser 318 with the liquid reservoir 331, and the contact dispenser 318 aspirates the reagent 332 from the liquid reservoir 331. Next, stage 320 aligns contact dispenser 318 with third plate 142, and contact dispenser 318 dispenses reagent 332 into wells 143 of third plate 142 to denature the pooled, normalized samples. Reagent 332 may be sodium hydroxide (NaOH). Other denaturing processes may prove suitable. For example, formamide or an equivalent may be used during the denaturing process.

[0294] System 300 may dilute the pooled and denatured samples after the pooling and denaturation processes have been performed. Contact dispenser 318 aspirates diluent 330 from liquid reservoir 331 in second work area 306. Stage 320 then aligns contact dispenser 318 with third plate 142, and contact dispenser 318 dispenses diluent 330 into wells 128 of third plate 142 to dilute samples 124 based on the sample concentration specified by the sequencing system (e.g., system 900) on which the samples are loaded. Pooled samples 124 in wells 143 of third plate 142 will have a concentration within the threshold after diluent 330 is added to wells 143. Diluent 330 may be a buffer.

[0295] System 300 may perform a loading process after the denaturation process and / or after the dilution process has been performed. Mover 144 moves third plate 142 from second work area 306 to plate receptacle 334 in loading area 308. Loading area 308 is shown including a stage 336 that can be used to move plate receptacle 334 relative to shipper assembly 174. Shipper assembly 174 flows the denatured sample from wells 128, 143, through corresponding shippers 184, through fluid lines 188, and out of system 300 to another system for sequencing (see, e.g., FIG. 24A).

[0296] While the above example discloses loading samples into a separate system 300, the system 300 may provide multiple options. For example, the system 300 may perform a library quantification process on the samples in a second work area 306, and the library of samples may be archived. The second work area 306 may be referred to as a common bay. Quantitation values ​​may be associated with and / or tracked with each library. The library of samples may be archived by sealing the samples and / or freezing the samples.

[0297] As another alternative, the system 300 may perform a library quantification process and a library pooling process on the samples in the second work area 306. The library pooling process may include preparing an equimolar pool using the samples based on the quantification values ​​determined by the library quantification process. The quantification values ​​may be used to determine, for example, what volumes of each sample should be used to create the equimolar pool. The system 300 may pipette different volumes of each sample into the pool based on the quantification values ​​to create the equimolar pool. The process may also include archiving the remainder of the library of samples.

[0298] In another alternative example, the system 300 may prepare a sequencing-ready pool of samples in the second work area 306. The sequencing-ready pool of samples can be prepared by performing a library quantification process and a library pooling process on the samples. The sequencing-ready pool of samples can be prepared, for example, by performing a denaturation process on the samples and / or performing a dilution process on the samples. The reagents used for denaturation and / or dilution can vary based on the sequencer type used. The final sequencing-ready concentration of the pool can vary based on the application (library type) and / or threshold loading concentration for the flow cell.

[0299] In another alternative example, system 300 may prepare a sequencing-ready pool of samples in second work area 306, and the sequencing-ready pool of a library of samples may be transferred to another system, such as a sequencer. System 300 and the other system (e.g., sequencer) may communicate and coordinate the transfer of the pool, for example, through fluid lines for sequencing.

[0300] System 300 also includes a drive assembly 173. Drive assembly 173 includes a pump drive assembly 219 and a valve drive assembly 220. Pump drive assembly 219 may be adapted to interact with pump 187 to pump fluid from reagent reservoir 110 to non-touch dispenser 146. Valve drive assembly 220 may be adapted to interface with valve 186 to control the position of valve 186.

[0301] Controller 176 includes a user interface 221, a communication interface 222, one or more processors 224, and a memory 226 that stores instructions executable by the one or more processors 224 to perform various functions discussed herein. User interface 221, communication interface 222, and memory 226 are electrically and / or communicatively coupled to the one or more processors 224. In some implementations, controller 176 may be located in the same area as other components of system 300 and physically coupled to the other components of system 300, e.g., via a wired connection. In other implementations, controller 176 may be located remotely from the other components of system 300 and communicatively coupled to the other components of system 300, e.g., via a wireless connection. For example, controller 176 may be implemented on a cloud computing device.

[0302] In one implementation, the user interface 221 can receive input from a user and provide the user with information associated with the operation of the system 300 (e.g., information about the analysis being performed). The user interface 221 can include a touchscreen, a display, a keyboard, a speaker, a mouse, a trackball, and / or a voice recognition system. The touchscreen and / or the display can display a graphical user interface (GUI).

[0303] In one implementation, communication interface 222 enables communication between system 300 and a remote system (e.g., a computer) over a network. The network may include the Internet, an intranet, a local area network (LAN), a wide area network (WAN), a coaxial cable network, a wireless network, a wired network (e.g., Ethernet), a satellite network, a digital subscriber line (DSL) network, a cellular network, a Bluetooth connection, a near field communication (NFC) connection, etc. For example, the library preparation system and the sequencer may be directly coupled to each other via a wired communication link (e.g., an Ethernet cable). The library preparation system can then send and receive communications to and from the sequencer via the wired communication link.

[0304] Some of the communications provided to the remote systems may be associated with, or generated or otherwise obtained by, system 300, amplification processes, cleanup processes, library normalization processes, pooling processes, denaturation processes, and / or loading processes, etc. Some of the communications provided to system 300 may be associated with, amplification processes, cleanup processes, library normalization processes, pooling processes, denaturation processes, and / or loading processes to be performed by system 300.

[0305] The one or more processors 224 and / or system 300 may include one or more of a processor-based system or a microprocessor-based system. In some implementations, the one or more processors 224 and / or system 300 include a reduced instruction set computer (RISC), an application-specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device that performs various functions, including those described herein.

[0306] The memory 226 may include one or more of a hard disk drive, flash memory, read-only memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), random access memory (RAM), non-volatile RAM (NVRAM) memory, compact disc (CD), digital versatile disc (DVD), cache, and / or any other storage device or storage disk on which information is stored for any period of time (e.g., permanently, temporarily, long-term, buffering, caching).

[0307] The memory 226 may store instructions executable on the processor 224 that configure the communication module of the library preparation system. The communication module of the library preparation system may send and receive communications to the sequencer via the communication interface 222, for example, using an Ethernet network. These communications may include information related to the library of samples. For example, the communication module of the library preparation system may send an indication of the preparation status of the library of samples to the sequencer. The preparation status may indicate that the library preparation is complete and the library of samples is ready to be loaded onto the sequencer. The preparation status may also include an estimated duration until the library preparation is complete.

[0308] The communication module of the library preparation system may also transmit to the sequencer the identification information (e.g., sample ID) of each sample in the library of samples. Additionally, for each sample, the communication module of the library preparation system may send to the sequencer an indication of an index attached to the sample. The index is a short fragment of DNA (e.g., 6-20 bases) attached to each sample that acts as a barcode or tag to identify and / or separate the sample within the library of samples.

[0309] Additionally, the communications module of the library preparation system may transmit instructions to the sequencer indicating the particular lane of the flow cell for each sample to be sequenced. For example, the flow cell may have eight lanes, and the communications module of the library preparation system may instruct the sequencer to place samples 1-10 in lane 1, samples 11-20 in lane 2, etc.

[0310] The communication module of the library preparation system may also transmit one or more run parameters to the sequencer so that the sequencer can sequence the library of samples using the received run parameters. The run parameters may include the number of cycles for each sample or any other suitable run parameters for sequencing.

[0311] Additionally, the communication module of the library preparation system may receive communications from the sequencer. For example, the communication module of the library preparation system can receive sequencer status information, such as whether the sequencer is ready to receive a library of samples, an estimated duration until the sequencer can reach a safe pause point in the sequencing recipe that will not cause data quality issues for any runs that have already been performed and can receive a library of samples, an indication of completed sequencing setup steps, remaining sequencing setup steps, the expected duration of remaining sequencing setup steps, etc. The communication module of the library preparation system can also receive acknowledgments of communications sent by the library preparation system from the sequencer. Additionally, the communication module of the library preparation system can send and receive any appropriate communications related to the library of samples to and from the sequencer.

[0312] The library preparation system and the sequencer can communicate back and forth to ensure that the sequencer is ready to receive the library of samples when library preparation is complete. For example, the library preparation system may send a communication to the sequencer indicating the preparation status of the library of samples. In response to receiving that communication, the sequencer can send a communication to the library preparation system indicating the estimated duration until the sequencer can receive the library of samples. This allows the library preparation system to plan its preparation steps to ensure sample integrity.

[0313] For example, if the library preparation system estimates that the library of samples will be prepared before the sequencer can receive the library of samples, the library preparation system may delay denaturing and diluting the samples until the sequencer is ready to receive the library of samples, or at least until within a threshold period of time that the sequencer is ready to receive the library of samples. The library preparation system may also store the samples until the sequencer is ready to receive the samples.

[0314] When a library preparation system prepares samples and performs sequencing steps before a sequencer receives the samples, the library preparation system and sequencer can provide updated estimates of the amount of time remaining until their respective devices are ready to load and receive samples, allowing the devices to adjust their preparation steps accordingly so that samples do not deteriorate while waiting for the sequencer and so that time is not wasted waiting for the sequencer to prepare the samples.

[0315] Then, when the library of samples is ready to be loaded into the sequencer and / or when the sequencer is ready to receive the library of samples, the library preparation system can send the library of samples to the sequencer through a fluid line configured to be coupled to the library preparation system and the sequencer, such as fluid line 188. For example, the library preparation system can send the library of samples to the sequencer through a fluid line in response to receiving an indication from the sequencer that the sequencer is ready to receive the library of samples.

[0316] FIG. 2 is a schematic diagram illustrating one implementation of another system 400 that can be used to implement the system 300 of FIG. 1. The system 400 of FIG. 2 is similar to the system 300 of FIG. 1. Like the system 300, the system 400 of FIG. 2 includes four consumable areas 302, four first work areas 304, one second work area 306, and one loading area 308. Each of the first work areas 304 may perform an amplification process and a cleanup process, and the second work area 306 may perform a quantification process, a library normalization process, a pooling process, a denaturation process, and / or a dilution process. The shipper assembly 174 may be used to transfer the prepared library to another system (e.g., a sequencing instrument).

[0317] Figure 3 is an isometric view illustrating one implementation of another system 500 that can be used to implement the system 300 of Figure 1. The system 500 of Figure 5 is similar to the system 400 of Figure 2 in that the system 500 of Figure 3 includes four consumable areas 302, four first work areas 304, one second work area 306, and one loading area 308.

[0318] FIG. 4 is a detailed isometric view of the system 500 of FIG. 3 showing the lid 322 removed from one of the work areas 302 and the lid 322 shown in another one of the work areas 302.

[0319] FIG. 5 is another detailed isometric view of the system 500 of FIG. 6 is another detailed isometric view of the system 500 of FIG. 3, showing the first work area 304, the actuator 324, the lid 322, and the contact dispenser 145. The first work area 304 includes a guide 501, including a track 502, that guides movement of the lid 322 between the retracted position shown and a position where the lid 322 is positioned over the receptacle 156. The contact dispenser 145 is shown as having twelve heads 504 that receive the tips 116.

[0320] 7 is another detailed isometric view of the system 500 of FIG. 3, showing two of the first work areas 304 and two of the contact dispensers 145. A portion of one of the contact dispensers 145 has been removed to more clearly show the internal workings of the contact dispenser 145.

[0321] 8 is a detailed isometric view of the system 500 of FIG. 3, showing the first work area 304 and the first plate receptacle 156. The plate receptacle 156 is shown to include a thermal block that defines a well receptacle, with the thermocycler 152 positioned below the well receptacle.

[0322] 9 is a detailed isometric view of the system 500 of FIG. 3 , showing the second work area 306 and a portion of the first work area 304. The second work area 306 includes the analyzer area 154 and a contact dispenser 318. The contact dispenser 318 includes a first head 506 carrying a first tip and a second head 508 carrying a second tip. The first head 506 may be used to aspirate / dispense a first volume of fluid, and the second head 508 may be used to aspirate / dispense a second volume of fluid. The contact dispenser 318 may include additional heads for carrying additional tips. For example, the contact dispenser 318 may include 12 heads 506 carrying 12 tips. The contact dispenser 318 may additionally or alternatively include or carry a non-contact dispenser (see, for example, non-contact dispenser 146 of FIG. 23).

[0323] FIG. 10 is a detailed isometric view of the system 500 of FIG. 3 , showing the loading area 308, which includes the sipper assembly 174 and a stage 336 that moves the plate receptacle 334 relative to the sipper assembly 174. The sipper assembly 174 includes a housing 509 that surrounds the sipper 184. The loading area 308 also includes a reagent cartridge receptacle 510 that, in the illustrated implementation, carries a reagent cartridge 512. The reagent cartridge 512 may, in some implementations, be a dry reagent cartridge that carries a flow cell. As used herein, a “flow cell” may include a device having a lid extending above a reaction structure to form flow channels therebetween that communicate with multiple reaction sites of the reaction structure, and may further include a detection device that detects a specified reaction occurring at or near the reaction sites. A contact dispenser 318 may be used to load a prepared library into the reagent cartridge 512.

[0324] 11 is a detailed isometric view of the system 500 of FIG. 3, showing the loading area 308 including the shipper assembly 174 with the housing 509 of the shipper assembly 174 removed to reveal the shipper 184. The plate receptacle 334 is shown carrying two plates 514, 516.

[0325] Figure 12 is a front view of another implementation of a system 600 that can be used to implement the system 300 of Figure 1. The system 600 of Figure 12 is similar to the system 500 of Figure 3 in that the system 600 of Figure 12 includes four consumable areas 302, four first work areas 304, one second work area 306, and one loading area 308. However, the loading area 308 is shown adjacent to and / or as part of the second work area 306 in the system 600 of Figure 12. A reagent cartridge receptacle 510 is also shown included in the system 600 of Figure 12 along with the second work area 306.

[0326] FIG. 13 is a top view of the system 600 of FIG. FIG. 14 is an isometric view of one of the consumable areas 302 and one of the first work areas 304 of the system 600 of FIG.

[0327] FIG. 15 is an isometric view of one of the consumable areas 302 implemented by a drawer 602 shown in the extended (or loading) position. FIG. 16 is a top view of one of the consumable areas 302 and one of the first work areas 304 of the system 600 of FIG.

[0328] FIG. 17 is a top view of one of the consumable areas 302 of the system 600 of FIG. 12. The consumable area 302 of FIG. 17 includes liquid reagents, bulk reagents, work plates, lyophilized reagents, and disposable tips. The lyophilized reagents may, in some implementations, include 12 columns and 12 rows of individual reagent containers. However, any number of columns and / or rows of lyophilized reagents may be provided. Each column (top and bottom as shown in FIG. 17) may be used when processing a single sample; thus, for example, the same and / or fewer pipette tips may be used during the amplification and / or cleanup process with less or no concern of cross-contamination.

[0329] Figure 18 is an isometric view of the contact dispenser 318, mover 144, and stage 320 of the system 600 of Figure 12. The stage 320 is mounted by a gantry 604 that allows the contact dispenser 318 and mover 144 to move in the x-direction 606, y-direction 608, and z-direction 610. The heads 506, 508 of the contact dispenser 318 may, in some implementations, be independently movable in the z-direction, thereby allowing the heads 506, 508 to be independently operable.

[0330] FIG. 19 is a top view of the second work area 306 and loading area 308 of the system 600 of FIG. Figure 20 is an isometric view showing one implementation of another system 700 that can be used to implement system 300 of Figure 1. System 700 of Figure 20 is similar to system 500 of Figure 3, except that system 700 of Figure 20 includes two consumable areas 302, two first work areas 304, one second work area 306, and one loading area 308. The loading area 308 and reagent cartridge receptacle 510 are shown on the side of system 700.

[0331] FIG. 21 is a detailed isometric view of the consumable area 302, the first work area 304, and the second work area 306 of the system 700 of FIG. FIG. 22 is a detailed isometric view of the consumable area 302, first work area 304, second work area 306, and loading area 308 of the system 700 of FIG.

[0332] 23 is a schematic diagram illustrating one implementation of another system 800 according to the teachings of the present disclosure. System 800 can be used, for example, to automatically, easily, and efficiently prepare DNA libraries for sequencing applications. In the illustrated implementation, system 800 includes consumable area 102, transfer area 104, work area 106, and reagent reservoir receptacle 108 for receiving reagent reservoir 110. Alternatively, reagent reservoir receptacle 108 may be located above work area 106.

[0333] The consumable area 102 includes a consumable receptacle 112, which is shown to receive a tip tray 114 having a first tip 116 and a second tip 118, a first plate 120 having wells 122 containing samples 124, and a second plate 126 having wells 128. The consumable receptacle 112 may be a drawer that can be pulled out of the system 800 and loaded with the consumables 114, 116, 118, 120, and 126. The consumable receptacle 112 is also shown receiving a lid 130, an index tray 132 having wells 134 containing indexes 136, and a bead tray 138 having wells 140 containing beads 141. The consumable area 102 may also have a third plate 142 having wells 143.

[0334] The first plate 120, the second plate 126, the index tray 132, and / or the bead tray 138 may be stacks of corresponding plates 120 and / or 126 and / or trays 132 and / or 138. The chip tray 116 may have a plurality of first chips 116, a plurality of second chips 118, and / or one or more chips of a different size than the first chips 116 and / or second chips 118. Although the chip tray 114 is described as having the first chips 116 and the second chips 118, the chip tray 114 can have any number of chips, such as 24 chips. However, the plates 120, 126 may have any number of wells.

[0335] Although plates 120 and 126 are described as having a single well 122, 128, plates 120, 126 may have multiple wells, such as 24 wells. Plates 120, 126, in some implementations, may include a 2×12 array of wells, allowing side access to all wells. Plates 120, 126 implemented with a 2×12 array allow loading levels / air bubbles to be inspected in all wells using side-view computer vision, increasing the chance of heat transfer in heating (PCR) operations and magnetic pull-down operations.

[0336] In the illustrated implementation, the transfer area 104 includes a mover 144, and the working area 106 includes a contact dispenser 145, a non-contact dispenser 146, a stage 148, a magnet 150, a thermocycler 152, and an analyzer area 154. The mover 144 may include a robotic arm. The non-contact dispenser 146 is fluidically coupled to the reagent reservoir 110. Alternatively, the non-contact dispenser 146 may use tips 116 and / or 118 to aspirate reagents from the reagent reservoir 110 and dispense the reagents into corresponding wells of the plates 120, 126. In such an implementation, the non-contact dispenser 146 may not be fluidically coupled to the reagent reservoir 110. The stage 148 may be an xy stage. Although the contact dispenser 145 and the non-contact dispenser 146 are shown schematically to the side of the stage 148, the contact dispenser 145 and the non-contact dispenser 146 may be located above the stage 148. The work area 106 may also include a light bar 155 that may be used to degrade oligonucleotides. In some implementations, the light bar 155 may be a high-power ultraviolet (UV) light bar that is used periodically throughout the workflow to repeatedly degrade oligonucleotides and prevent cross-contamination.

[0337] The stage 148 has a first plate receptacle 156, a second plate receptacle 158, and a third plate receptacle 159, and the analyzer area 154 includes a substrate 162 and an imaging system 164. The plate receptacles 156, 158, and 159 may be referred to as plate stations. The imaging system 164 may be a fluorescence imaging system, i.e., a fluorescence spectrophotometer including an objective lens and / or a solid-state imaging device. The solid-state imaging device may include a charge-coupled device (CCD) and / or a complementary metal-oxide semiconductor (CMOS). The stage 148 may also include a wash station 165, which may be used to wash and / or rinse the chips 116 and / or 118 between successive interfaces to the sample / reagents, for example, to prevent cross-contamination between reagents. Alternatively, the wash station 165 may be omitted. Stage 148 is shown as including three plate receptacles 156, 158, 159, but may include any number of plate receptacles, such as six plate receptacles.

[0338] In some implementations, system 800 can perform DNA library preparation workflows, including amplification processes, cleanup processes, library normalization processes, and / or pooling processes. System 800 can perform workflows such as whole genome sequencing (WGS) workflows, DNA and RNA enrichment workflows, methylation workflows, split-pool amplicon workflows, and / or amplicon workflows. DNA library preparation workflows can be performed on any number of samples (e.g., from 1 sample to 24 samples). Thus, system 800 enables variable batch processing.

[0339] The mover 144 moves the tip tray 114, the first plate 120, the second plate 126, the lid 130, and the index tray 132 during operation to perform workflow processes between the consumable area 102 and the work area 106, and the stage 148 aligns the first plate receptacle 156, the second plate receptacle 158, and the third plate receptacle 159 with respect to the contact dispenser 145 and the non-contact dispenser 146. The system 800 also includes an actuator 166, a door 168, a gas source 170, a valve 172, a drive assembly 173, a sipper assembly 175, and a controller 176. The gas source 170 is fluidly coupled to the reagent reservoir 110. Alternatively, the actuator 166, the door 168, and / or the gas source 170 may be omitted.

[0340] A door 168 is movable to surround the reagent reservoir receptacle 108, and an actuator 166 moves the magnet 150 relative to the second plate receptacle 158. The actuator 166 can move the magnet 150 between an upper position, in which the magnet 150 affects any plates placed on the second plate receptacle 158, and a lower position, in which the magnet 150 does not affect any plates placed on the second plate receptacle 158. Moving the magnet 150 relative to the second plate receptacle 158 and any plates 120, 126, 142 placed on the second plate receptacle 158 allows less area on the work area 106 to be consumed. The magnet 150 can also move one of the sample-loaded plates 120, 126, 142 with a relatively high degree of reliability compared to alternative approaches that move one of the sample-loaded plates 120, 126, 142 to a separate magnet station. The magnets 150 may be implemented in a Halbach array configuration to strengthen and focus the corresponding magnetic field.

[0341] Valve 172 controls the flow of gas 178 from gas source 170 to reagent reservoir receptacle 108. Gas 178 can include nitrogen. Door 168 encloses reagent reservoir receptacle 108, protecting reagent reservoir 110 and the reagents 180 contained therein from exposure to ambient light. Reagent reservoir receptacle 108 can be filled with gas 178 and / or exposed to less ambient light, protecting the reagents 180 contained therein from exposure to atmospheric gases, such as oxygen, and / or from reduced exposure to ambient gases. Thus, the environment, such as the temperature of reagent reservoir receptacle 108, can be temperature controlled. Reagent reservoir 110 storing reagents 180 at a controlled temperature allows reagents 180 to be stored on system 800 for a threshold amount of time, such as weeks.

[0342] The sipper assembly 175 may be coupled to a corresponding number of reagent reservoirs 110 via reagent sippers 185. The reagent reservoirs 110 may contain fluids (e.g., reagents and / or other reaction components). The sipper assembly 175, in some implementations, includes multiple ports, and each port of the sipper assembly 175 may receive one of the reagent sippers 185. The reagent sippers 185 may be referred to as fluid lines. The sipper assembly 175 also includes valves 186 that may be selectively actuated to control fluid flow through the fluid lines 188. The fluid lines 188 may include multiple fluid lines, with each fluid line 188 being used to flow, for example, one sample. The sipper assembly 175 also includes a pump 187 for selectively flowing reagents 180 from the reagent reservoirs 110, through the reagent sippers 185, through the fluid lines 188, and out of the non-contact dispenser 146. The pump 187 may additionally or alternatively be used to actuate the valve of the contactless dispenser 146 .

[0343] Valve 186 may be implemented by a rotary valve, a pinch valve, a flat valve, a solenoid valve, a check valve, a piezoelectric valve, or the like. Other fluid control devices may prove suitable. Pump 187 may be implemented by a syringe pump, a peristaltic pump, and / or a diaphragm pump. However, other types of fluid transfer devices may be used. Controller 176 is electrically and / or communicatively coupled to mover 144, thermocycler 152, actuator 166, imaging system 164, contact dispenser 145, non-contact dispenser 146, sipper assembly 175, valve 186, pump 187, door 168, and drive assembly 173 to perform various functions as disclosed herein. Alternatively, sipper assembly 175 may be omitted.

[0344] In some implementations, the mover 144 moves the tip tray 114 from the consumable area 102 to the first plate receptacle 156, the first plate 120 from the consumable area 102 to the second plate receptacle 158, and the index tray 132 from the consumable area 102 to the third plate receptacle 159 to begin the DNA library preparation workflow. Different wells 122 of the first plate 120 may contain different samples 124. The samples 124 may be biological samples of human, animal, plant, bacterial, or fungal origin. Other sources of biological samples may prove suitable. The mover 144 may include a gantry with grippers that can pick up and place objects, such as plates 120, 126 and / or trays 132, 138, between different areas 102, 104, 106 of the system 800. However, the mover 144 may be implemented differently.

[0345] The stage 148 aligns the contact dispenser 145 with the tip tray 114, and the contact dispenser 145 couples with a first tip 116 from the tip tray 114. Although the contact dispenser 145 is described as coupling with one first tip 116, the contact dispenser 145 may couple with a number of first tips 116 corresponding to the number of wells 122 in the first plate 120 and / or the number of wells 122 in the first plate 120 that contain samples 124. For example, the first tip 116 may be a smaller pipette tip used to transfer smaller fluid volumes, and the second tip 118 may be a larger pipette tip used to transfer larger fluid volumes. Each of the first tip portion 116 and / or second tip portion 118 may only be exposed to a single sample during a workflow, thereby reducing the possibility of cross-contamination. Each of the first tip 116 and / or the second tip 118 may be used throughout a workflow. The contact dispenser 145 may be coupled to and / or use different ones of the tips 116, 118 depending on the workflow that the system 800 is implementing and / or depending on the processes within the workflow.

[0346] Stage 190 is coupled to contact dispenser 145 and can move contact dispenser 145 to allow contact dispenser 145 to couple with tip portions 116, 118. Stage 190 may be a z-stage. Alternatively, stage 190 may be omitted. Stage 148 aligns contact dispenser 145 with index tray 132, and contact dispenser 145 uses first tip 116 to aspirate index 136 from index tray 132. Stage 148 can then align contact dispenser 145 with first plate 120, and contact dispenser 145 dispenses index 136 into well 122 of first plate 120. The mover 144 moves the lid 130 from the consumable area 102 and places the lid 130 on the first plate 120, covering the wells 122 of the first plate 120. Alternatively, the lid 130 may be movably coupled to the thermocycler 152. In such an implementation, the lid 130 may not be disposable.

[0347] The thermocycler 152 is aligned with the second plate receptacle 158, and the thermocycler 152 amplifies the samples 124 in the wells 122 of the first plate 120. In the illustrated implementation, the thermocycler 152 is carried by the stage 148. Thus, the thermocycler 152 and / or the magnet 150 can act on the plates 120, 126 received in the second plate receptacle 158. Alternatively, the thermocycler 152 may be positioned remote from the magnet 150 and / or may not be carried by the stage 148.

[0348] The mover 144 can move the lid 130 from the first plate 120 to the consumable area 102 after the amplification process, and the mover 144 moves the index tray 132 from the third plate receptacle 159 to the consumable area 102. The consumable area 102 includes a waste tray 192 that can receive used consumables, such as the lid 130. However, alternatively, the lid 130 may be reused. The waste tray 192 may be a waste tray having an absorbent material that absorbs liquid waste.

[0349] The system 800 can perform a cleanup process after the amplification process is performed. In some implementations, the mover 144 moves the bead tray 138 from the consumable area 102 to the third plate receptacle 159 to begin the cleanup process. The stage 148 aligns the contact dispenser 145 with the bead tray 138, and the contact dispenser 145 aspirates the beads 141 from the bead tray 138. The contact dispenser 145 may aspirate the beads 141 using the same first tip 116 used to aspirate the index 136. Alternatively, the contact dispenser 145 may use another one of the first tips 116 or one of the second tips 118 to aspirate the beads 141.

[0350] Stage 148 aligns contact dispenser 145 with first plate 120, which dispenses beads 141 into wells 140 of first plate 120 as part of a cleanup process. Stage 148 aligns non-contact dispenser 146 with first plate 120, which dispenses first reagent 194 from reagent reservoir 110 into wells 122 of first plate 120. First reagent 194 may be a bead buffer, and sample 124 may bind to beads 141 in the presence of the bead buffer. In some implementations, non-contact dispenser 146 may be capable of jet dispensing at a liquid velocity appropriate to enable jet mixing. The precision of non-contact dispenser 146 may allow fewer reagents to be used compared to a manual workflow; for example, the amount of reagent that can be used may be approximately one-quarter to one-half. The non-contact dispenser 146 can deliver a volume of reagent of about 1 μL with a coefficient of variation (CV) precision error of less than about 2% and a precision error of less than about 4%, in some examples, such that the total fluid volume error is less than about 10%. For larger volume delivery, the non-contact dispenser 146 may deliver about 50 μL to each well 122 of the first plate 120 in about 48 seconds (sec), and for smaller volume delivery, it may deliver about 5 μL to each well 122 of the first plate 120 in about 24 seconds (sec).

[0351] A stage 196 can be coupled to the non-contact dispenser 146 and move the non-contact dispenser 146 to enable the non-contact dispenser 146 to dispense a liquid, such as a first reagent 194, into the wells 122 of the first plate 120. The first reagent 194 can be a bead buffer, and the sample 124 can bind to the beads 141 in the presence of the first reagent 194. The stage 196 can be a z-stage or an xyx-stage in some implementations. In implementations in which the non-contact dispenser 146 is coupled to the chips 116 and / or 118 and the non-contact dispenser 146 is positioned to aspirate the reagent 180 directly from the reagent reservoir 110, the stage 196 can be an xyz-stage. Alternatively, the stage 196 can be omitted.

[0352] The stage 148 aligns the contact dispenser 145 with the tip tray 114, the contact dispenser 145 places a first tip 116 into the tip tray 114, and then the contact dispenser 145 mates with a second tip 118 from the tip tray 114. Although the contact dispenser 145 is described as mateable with one second tip 118, the contact dispenser 145 may mate with a number of second tips 118 corresponding to the number of wells 122 in the first plate 120 and / or the number of wells 122 in the first plate 120 that contain samples 124.

[0353] Actuator 166 moves magnet 150 toward second plate receptacle 158, and magnet 150 attracts beads 141 toward magnet 150. Beads 141 and samples 124 bound to beads 141 can be positioned toward the bottom of wells 122 of first plate 120 or on the sides of wells 122. Chips 116 and / or 118 can easily access wells 122 when beads 141 are on the sides of wells 122. However, magnet 150 can position beads 141 anywhere within wells 122.

[0354] The stage 148 aligns the contact dispenser 145 with the first plate 120, and the contact dispenser 145 aspirates the first reagent 194 from the wells 122 of the first plate 120. The mover 144 can move the bead tray 138 from the third plate receptacle 159 to the consumable area 102. The mover 144 can move the waste 192 to the third plate receptacle 159, and the contact dispenser 145 can dispense the first reagent 194 aspirated from the wells 122 of the first plate 120 into the waste 192. The mover 144 can return the waste 192 to the consumable area 102.

[0355] Stage 148 aligns non-contact dispenser 146 with first plate 120, and non-contact dispenser 146 dispenses second reagent 198 from reagent reservoir 110 into wells 122 of first plate 120. Second reagent 198 may be an elution buffer that releases sample 124 from its binding to beads 141, and specifically, releases DNA associated with sample 124 from its binding to beads 141.

[0356] The mover 144 moves the second plate 126 from the consumable area 102 to the third plate receptacle 159. The system 800 can use the second plate 126 for transfer operations. The actuator 166 moves the magnet 150 toward the second plate receptacle 158, attracting the beads 141 toward the magnet 150, thus suspending the second reagent 198 and the sample 124 within the well 122.

[0357] The stage 148 aligns the contact dispenser 145 with the first plate 120, and the contact dispenser 145 aspirates, for example, using the second tip 118, the second reagent 198 and the sample 124 from the wells 122 of the first plate 120. The stage 148 aligns the contact dispenser 145 with the second plate 126, and the contact dispenser 145 dispenses the second reagent 198 and the sample 124 into the wells 128 of the second plate 126.

[0358] The system 800 can perform a quantification process after the cleanup process is performed. In some implementations, the stage 148 aligns the contact dispenser 145 with the tip tray 114 to begin the quantification process, the contact dispenser 145 places the second tip 118 into the tip tray 114, and the contact dispenser 145 combines with the first tip 116 from the tip tray 114.

[0359] In the illustrated implementation, the substrate 162 of the analyzer area 154 is carried by the stage 148, and the imaging system 164 is spaced from the stage 148 and coupled to a portion of the system 800, such as a frame of the system 800. Alternatively, the imaging system 164 may be carried by the stage 148. The substrate 162 is shown to include a pair of plates 200, 202 having a gap 204 defined therebetween. The substrate 162 also has an inlet 206 and an outlet 208 in fluid communication with the gap 204, and a seal 210 disposed between the pair of plates 200, 202. The plates 200, 202 and the seal 210 define a channel 212 between the inlet 206 and the outlet 208. A waste reservoir 214 is fluidly coupled to the outlet 208 of the substrate 162 by a fluid line 216.

[0360] To perform the quantification process, stage 148 aligns contact dispenser 145 with second plate 126, and contact dispenser 145 aspirates second reagent 198 and a portion of sample 124 from well 128 of second plate 126. The second reagent 198 and the portion of sample 124 may be approximately 2 μL.

[0361] The stage 148 aligns the contact dispenser 145 with the inlet 206 of the substrate 162, and the contact dispenser 145 dispenses the second reagent 198 and a portion of the sample 124 into the inlet 206 of the substrate 162. In this embodiment, the second reagent 198 and the portion of the sample 124 may flow and / or be disposed between the inlet 206 and the outlet 208, and the imaging system 164 acquires image data of the second reagent 198 and the portion of the sample 124. The imaging system 164 and / or the system 800 use the image data to determine the concentration of the sample 124. Negative pressure, oil, and / or another substance may be used to bias the second reagent 198 and the portion of the sample 124 between the inlet 206 and the outlet 208. Alternatively, before the first plate 200 is placed on the second plate 202, the first plate 200 may be hingedly or removably coupled to the second plate 202 to enable the contact dispenser 145 to dispense a portion of the second reagent 198 and sample 124 onto the second plate 202.

[0362] The system 800 may perform a normalization process after the quantification process is performed. In some implementations, the stage 148 aligns the second plate 126 with the non-contact dispenser 146 to begin the normalization process. The non-contact dispenser 146 dispenses a diluent 218 into the wells 128 of the second plate 126 to dilute the sample 124 based on the determined sample concentration. The sample 124 in the wells 128 of the second plate 126 will have a concentration within the threshold after the diluent 218 is added to the wells 128. The diluent 218 may be a buffer.

[0363] The system 800 may perform a pooling process after the quantification process is performed. In some implementations, the stage 148 aligns the contact dispenser 145 with the tip tray 114, the contact dispenser 145 places a first tip 116 into the tip tray 114, and then the contact dispenser 145 couples with a second tip 118 from the tip tray 114 to begin the pooling process. The mover 144 moves the tip tray 114 from the first plate receptacle 156 to the consumable area 102, and the mover 144 moves the third plate 142 to the first plate receptacle 156. The stage 148 aligns the second plate 126 with the contact dispenser 145, and the contact dispenser 145 aspirates the sample 124 from the well 128 of the second plate 126. Stage 148 then aligns third plate 142 with contact dispenser 145, which dispenses sample 124 into well 143 of third plate 142. Additional samples from other wells of second plate 126 can be deposited into wells 143 of third plate 142 in a similar manner to combine multiple normalized samples together. A single tip can be used for the pooling process.

[0364] The drive assembly 173 includes a pump drive assembly 219 and a valve drive assembly 220. The pump drive assembly 219 may be adapted to interact with the pump 187 to pump fluid from the reagent reservoir 110 to the non-touch dispenser 146. The valve drive assembly 220 may be adapted to interface with the valve 186 to control the position of the valve 186.

[0365] Controller 176 includes a user interface 221, a communication interface 222, one or more processors 224, and a memory 226 that stores instructions executable by the one or more processors 224 to perform various functions, including the disclosed implementations. User interface 221, communication interface 222, and memory 226 are electrically and / or communicatively coupled to the one or more processors 224.

[0366] In one implementation, the user interface 221 receives input from a user and provides the user with information associated with the operation of the system 800 and / or the analysis being performed. The user interface 221 may include a touchscreen, a display, a keyboard, a speaker, a mouse, a trackball, and / or a voice recognition system. The touchscreen and / or the display may display a graphical user interface (GUI).

[0367] In one implementation, communication interface 222 enables communication between system 800 and a remote system (e.g., a computer) using a network. The network may include an intranet, a local area network (LAN), a wide area network (WAN), an intranet, etc. Some of the communications provided to the remote system may be associated with, or generated by, system 800, an amplification process, a cleanup process, a library normalization process, and / or a pooling process, etc. Some of the communications provided to system 800 may be associated with, an amplification process, a cleanup process, a library normalization process, and / or a pooling process performed by system 800.

[0368] The one or more processors 224 and / or system 800 may include one or more of a processor-based system or a microprocessor-based system. In some implementations, the one or more processors 224 and / or system 800 include a reduced instruction set computer (RISC), an application-specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device that performs various functions, including those described herein. The memory 226 may include one or more of a hard disk drive, flash memory, read-only memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), random access memory (RAM), non-volatile RAM (NVRAM) memory, compact disc (CD), digital versatile disc (DVD), cache, and / or any other storage device or storage disk on which information is stored for any period of time (e.g., permanently, temporarily, long-term, buffering, caching).

[0369] 24A is a schematic diagram illustrating one implementation of another system 900 according to the teachings of the present disclosure. System 900 may be a sequencing system and / or a next-generation sequencing (NGS) system. System 900 can be used to perform analysis on one or more target samples. The samples may include one or more DNA clusters linearized to form single-stranded DNA (sstDNA). In the illustrated implementation, system 900 is adapted to receive a pair of flow cell assemblies 902, 904 including corresponding flow cells 906, and includes, in part, an imaging system 908 and a flow cell interface 910 having flow cell receptacles 912, 914 that support the corresponding flow cell assemblies 902, 904. Flow cell interface 910 may be associated with and / or referred to as a flow cell deck structure. The system 900 also includes a stage assembly 916, a pair of reagent selector valve assemblies 918, 920, each including a reagent selector valve 922 and a valve driver assembly 924, and a controller 926. The reagent selector valve assemblies 918, 920 may be referred to as mini-valve assemblies. The controller 926 is electrically and / or communicatively coupled to the imaging system 908, the reagent selector valve assemblies 918, 920, and the stage assembly 916, and is adapted to cause the imaging system 908, the reagent selector valve assemblies 918, 920, and the stage assembly 916 to perform various functions as disclosed herein.

[0370] In this implementation, the reagent selector valve assemblies 918, 920 are carried by the flow cell interface 910 and are positioned directly adjacent to the corresponding flow cell assemblies 902, 103. The proximity between the reagent selector valve assemblies 918, 920 and the corresponding flow cell assemblies 902, 103 allows for reduced reagent consumption, for example, reduced dead volume in the fluid lines, reduced carryover, reduced switching time, and / or results per hour. The stage assembly 916 includes an x-motor and ball screw 928 that moves the flow cell interface 910 in the x-direction relative to the imaging system 908, and a y-motor and ball screw 930 that moves the flow cell interface 910 in the y-direction relative to the imaging system 908.

[0371] 24A , in the illustrated implementation, system 900 also includes a sipper assembly 934, a sample loading assembly 936, a pump manifold assembly 938, a drive assembly 940, and a waste reservoir 942. Controller 926 is electrically and / or communicatively coupled to sipper assembly 934, sample loading assembly 936, pump manifold assembly 938, and drive assembly 940 and adapted to cause sipper assembly 934, sample loading assembly 936, pump manifold assembly 938, and drive assembly 940 to perform various functions as disclosed herein. Sample loading assembly 936 may include a sample port 1001 and a flow cell port 1003.

[0372] The controller 926 may also be electrically and / or communicatively coupled to the controller 176 of another system (e.g., systems 300, 400, 500, 600, 700, 800). The sample loading assembly 936 may be referred to as a sample manifold loading assembly.

[0373] Referring to the flow cells 906, in the illustrated implementation, each of the flow cells 906 includes a plurality of channels 944, each having a first channel opening disposed at a first end of the flow cell 906 and a second channel opening disposed at a second end of the flow cell 906. Depending on the direction of flow through the channels 944, either of the channel openings can act as an inlet or an outlet. Although the flow cell 906 is shown in Figure 24A as including two channels 944, any number of channels 944 (e.g., 1, 2, 6, 8) can be included.

[0374] Each of the flow cell assemblies 902, 904 also includes a flow cell frame 946 and a flow cell manifold 948 coupled to a first end of the corresponding flow cell 906. As used herein, a "flow cell" (also referred to as a flow cell) can include a device having a lid extending over a reaction structure to form a flow channel between the flow cells that communicates with multiple reaction sites of the reaction structure. Some flow cells can also include a detection device to detect a specified reaction occurring at or adjacent to the reaction site. As shown, the flow cell 906, the flow cell manifold 948, and / or any associated gaskets used to establish a fluid connection between the flow cell 906 and the system 900 are coupled to or otherwise supported by the flow cell frame 946. While the flow cell frame 946 is shown included in the flow cell assemblies 902, 904 in FIG. 24A , the flow cell frame 946 can be omitted. In this manner, the flow cell 906 and associated flow cell manifold 948 and / or gasket may be used in the system 900 without the flow cell frame 946 .

[0375] In some implementations, components of system 900 that are shown only once and that are coupled to both of flow cells 906 may be replicated such that each flow cell 906 has its own corresponding components. For example, each flow cell 906 may be associated with a separate sample loading assembly 936, pump manifold assembly 938, etc. In other implementations, system 900 may include a single flow cell 906 and corresponding components.

[0376] System 900, in the illustrated implementation, is fluidly coupled to another system (e.g., systems 300, 400, 500, 600, 700, 800) by fluid lines 188, which, in the illustrated implementation, carry one or more samples of interest (e.g., analytes, libraries) to a sample manifold assembly 936. Although two fluid lines 188 are shown, any other number of fluid lines 188 may be included.

[0377] The sample loading assembly 936 includes one or more sample valves 954, and the pump manifold assembly 938 includes one or more pumps 956, one or more pump valves 958, and a cache 960. One or more of the valves 954, 958 may be implemented by rotary valves, pinch valves, flat valves, solenoid valves, check valves, piezoelectric valves, two-way valves, three-way valves, electrically actuated valves, pneumatically actuated valves, and combinations thereof. However, different types of fluid control devices may be used. One or more of the pumps 956 may be implemented by syringe pumps, peristaltic pumps, and / or diaphragm pumps. However, other types of fluid transfer devices may be used. The cache 960 may be a serpentine cache and may temporarily store one or more reaction components, for example, during a bypass operation of the system 900 of FIG. 24A. While the cache 960 is shown included in the pump manifold assembly 938, in another implementation, the cache 960 may be located in a different location. For example, cache 960 may be included within shipper assembly 934 or within another manifold downstream of bypass fluid line 962 .

[0378] A sample loading assembly 936 and a pump manifold assembly 938 direct one or more samples of interest from other systems (eg, systems 300, 400, 500, 600, 700, 800) through fluid line 964 toward the flow cell assemblies 902, 904.

[0379] The fluid lines 964 may be referred to as flow cell fluid lines. In some implementations, the sample loading assembly 936 can individually load / direct a sample of interest into each channel 944 of the flow cell 906. The process of loading a sample of interest into the channels 944 of the flow cell 906 may be performed automatically using the system 900 of FIG. 24A.

[0380] The sample loading assembly 936 may draw one or more target samples through the sample fluid line 188 and through the sample port 1001. The sample loading assembly 936 can then flow the one or more target samples through the sample port 1003, the flow cell fluid line 964, and toward the flow cell assemblies 902, 904. Each sample fluid line 188 and each flow cell fluid line 964 may be associated with one channel of the flow cell assemblies 902, 904.

[0381] 24A , the sample loading assembly 936 is positioned downstream of the flow cell assemblies 902, 904. Thus, the sample loading manifold assembly 936 can load the target sample into the flow cell 906 from the rear of the flow cell 906. Loading the target sample from the rear of the flow cell 906 can be referred to as “rear loading.” Rear-loading the target sample into the flow cell 906 can reduce contamination. In the illustrated implementation, the sample loading assembly 936 is coupled between the flow cell assemblies 902, 904 and the pump manifold assembly 938.

[0382] To draw a sample of interest from another system (e.g., systems 300, 400, 500, 600, 700, 800) toward pump manifold assembly 938, sample valve 954, pump valve 958, and / or pump 956 can be selectively actuated to urge the sample of interest toward pump manifold assembly 938. Fluid line 188 may include multiple sample fluid lines coupled between sipper 184 of sipper assembly 174 and selectively fluidly accessible via corresponding sample valves 954. Thus, each sample can be selectively separated from the other samples using the corresponding fluid line and / or corresponding sample valve 954.

[0383] The sample valves 954, pump valves 958, and / or pumps 956 can be selectively actuated to force the target samples toward the flow cell assembly 902 and into each channel 944 of the corresponding flow cell 906 to individually flow the target samples toward the corresponding channel of one of the flow cells 906 and away from the pump manifold assembly 938. In some implementations, each channel 944 of the flow cell 906 receives a target sample. In other implementations, one or more of the channels 944 of the flow cell 906 selectively receive the target sample, while others of the channels 944 of the flow cell 906 do not receive the target sample. The channels 944 of the flow cell 906 that cannot receive the target sample can instead receive a wash buffer, for example.

[0384] A drive assembly 940 interfaces with the shipper assembly 934 and the pump manifold assembly 938 to flow one or more reagents that interact with the sample in the corresponding flow cell 906. In one implementation, reversible terminators are attached to the reagents to allow incorporation of a single nucleotide onto the growing DNA strand. In some such implementations, one or more of the nucleotides have a unique fluorescent label that emits a color when excited. The color (or lack thereof) is used to detect the corresponding nucleotide. In the illustrated implementation, the imaging system 908 excites one or more of the distinguishable labels (e.g., fluorescent labels) and then acquires image data of the distinguishable labels. The labels can be excited by incident light and / or a laser, and the image data can include one or more colors emitted by each label in response to excitation. The image data (e.g., detection data) can be analyzed by the system 900. The imaging system 908 can be a fluorescence spectrophotometer including an objective lens and / or a solid-state imaging device. The solid-state imaging device may include a charge-coupled device (CCD) and / or a complementary metal-oxide semiconductor (CMOS). However, other types of imaging systems and / or optics may be used. For example, the imaging system 908 may be or be associated with a scanning electron microscope, a transmission electron microscope, an imaging flow cytometer, high-resolution optical microscopy, confocal microscopy, epifluorescence microscopy, two-photon microscopy, differential interference contrast microscopy, etc.

[0385] After the image data is acquired, the drive assembly 940 interfaces with the sipper assembly 934 and the pump manifold assembly 938 to flow another reaction component (e.g., a reagent) through the flow cell 906, which is then received by a waste reservoir 942 via a main waste line 966 and / or otherwise discharged by the system 900. Some reaction components perform a flushing action that chemically cleaves the fluorescent label and reversible terminator from the sstDNA. The sstDNA is then ready for another cycle.

[0386] A main waste line 966 is coupled between the pump manifold assembly 938 and the waste reservoir 942. In some implementations, pumps 956 and / or pump valves 958 of the pump manifold assembly 938 selectively flow reaction components from the flow cell assemblies 902, 904 through the fluid lines 964 and the sample loading manifold assembly 936 to the main waste line 966.

[0387] The flow cell assemblies 902, 904 are coupled to a central valve 968 via a flow cell interface 910. An auxiliary waste line 970 is coupled to the central valve 968 and to a waste reservoir 942. In some implementations, the auxiliary waste line 970 receives excess fluid of the sample of interest from the flow cell assemblies 902, 904 via the central valve 968 when the sample of interest is back-loaded into the flow cell 906, as described herein, and directs the excess fluid of the sample of interest to the waste reservoir 942. That is, the sample of interest can be loaded from the back of the flow cell 906, and any excess fluid of the sample of interest can flow out the front of the flow cell 906. By rear-loading the flow cells 906 with the target samples, different samples can be separately loaded into corresponding channels 944 of corresponding flow cells 906, and a single flow cell manifold 948 can connect the front of the flow cells 906 to a central valve 968 and direct excess fluid from each target sample to an auxiliary waste line 970. Once the target samples are loaded into the flow cells 906, the flow cell manifold 948 can be used to deliver a common reagent from the front (e.g., upstream) of the flow cell 906 to each channel 944 of the flow cell 906, with this common reagent exiting the rear (e.g., downstream) of the flow cell 906. In other words, the target sample and reagent can flow in opposite directions through the channels 944 of the flow cell 906.

[0388] Referring to the sipper assembly 934, in the illustrated implementation, the sipper assembly 934 includes a shared line valve 972 and a bypass valve 974. The shared line valve 972 may be referred to as a reagent selector valve. The valve 922 of the reagent selector valve assemblies 918, 920, the central valve 968, and / or the valves 972, 974 of the sipper assembly 934 may be selectively actuated to control fluid flow through the fluid lines 976, 977, 978, 979, 980. One or more of the valves 922, 958, 968, 972, 974 may be implemented by rotary valves, pinch valves, flat valves, solenoid valves, check valves, piezoelectric valves, etc. Other fluid control devices may prove suitable.

[0389] The sipper assembly 934 can be coupled to a corresponding number of reagent reservoirs 982 via reagent sippers 984. The reagent reservoirs 982 can contain fluids (e.g., reagents and / or other reaction components). In some implementations, the sipper assembly 934 includes multiple ports. Each port of the sipper assembly 934 can receive one of the reagent sippers 984. The reagent sippers 984 can be referred to as a fluid line.

[0390] The shared line valve 972 of the sipper assembly 934 is coupled to the central valve 968 via a shared reagent fluid line 976. Different reagents may flow through the shared reagent fluid line 976 at different times. In one implementation, when performing a flushing operation before changing one reagent for another, the pump manifold assembly 938 may draw a wash buffer through the shared reagent fluid line 976, the central valve 968, and the corresponding flow cell assemblies 902, 904. Thus, the shared reagent fluid line 976 may be involved in the flushing operation. Although one shared reagent fluid line 976 is shown, any number of shared fluid lines may be included in the system 900.

[0391] The bypass valve 974 of the sipper assembly 934 is coupled to the central valve 968 via reagent fluid lines 977, 978. The central valve 968 may have one or more ports that correspond to the reagent fluid lines 977, 978.

[0392] Dedicated fluid lines 979, 980 are coupled between the sipper assembly 934 and the reagent selector valve assemblies 918, 920. Each of the dedicated reagent fluid lines 979, 980 may be associated with a single reagent. Fluids that may flow through the dedicated reagent fluid lines 979, 980 may be used during sequencing operations and may include cleavage reagents, incorporation reagents, scanning reagents, cleavage wash solutions, and / or wash buffers. Because only a single reagent may flow through each of the dedicated reagent fluid lines 979, 980, the dedicated reagent fluid lines 979, 980 themselves do not need to be flushed when performing a flushing operation before switching between one reagent and another. Including dedicated reagent fluid lines 979, 980 may be advantageous when the system 900 uses reagents that may have adverse reactions with other reagents. Furthermore, reducing the number of fluid lines or the length of the fluid lines that are flushed when changing between different reagents can reduce reagent consumption and flush volumes, thereby decreasing the cycle time of the system 900. Although four dedicated reagent fluid lines 979 , 980 are shown, any number of dedicated fluid lines may be included in the system 900 .

[0393] The bypass valve 974 is also coupled to the cache 960 of the pump manifold assembly 938 via a bypass fluid line 962. One or more reagent priming, hydration, mixing, and / or transfer operations may be performed using the bypass fluid line 962. The priming, hydration, mixing, and / or transfer operations may be performed independently of the flow cell assemblies 902, 904. Thus, operations using the bypass fluid line 962 may be performed, for example, during incubation of one or more samples of interest in the flow cell assemblies 902, 904. That is, the shared line valve 972 may be utilized independently of the bypass valve 974, such that the bypass valve 974 may utilize the bypass fluid line 962 and / or the cache 960 to perform one or more operations while the shared line valve 972 and / or the central valve 968 are performing other operations simultaneously, substantially simultaneously, or offset-synchronously. Thus, the system 900 may perform multiple operations at once, thereby reducing execution time.

[0394] Referring now to drive assembly 940, in the illustrated implementation, drive assembly 940 includes a pump drive assembly 986 and a valve drive assembly 988. Pump drive assembly 986 may be adapted to interface with one or more pumps 956 to pump fluid through and / or load one or more samples of interest into flow cell 906. Valve drive assembly 988 may be adapted to interface with one or more of valves 954, 958, 968, 972, 974 to control the position of the corresponding valves 954, 958, 968, 972, 974.

[0395] Referring to the controller 926, in the illustrated implementation, the controller 926 includes a user interface 990, a communication interface 992, one or more processors 994, and a memory 996 that stores instructions executable by the one or more processors 994 to perform various functions, including the disclosed implementations. The user interface 990, the communication interface 133, and the memory 996 are electrically and / or communicatively coupled to the one or more processors 994.

[0396] In one implementation, the user interface 990 is adapted to receive input from a user and provide the user with information associated with the operation of the system 900 and / or the analyses performed. The user interface 990 may include a touchscreen, a display, a keyboard, a speaker, a mouse, a trackball, and / or a voice recognition system. The touchscreen and / or the display may display a graphical user interface (GUI).

[0397] In one implementation, the communications interface 992 is adapted to enable communication between the system 900 and a remote system (e.g., a computer, a library preparation system) over a network. The network may include the Internet, an intranet, a local area network (LAN), a wide area network (WAN), a coaxial cable network, a wireless network, a wired network (e.g., Ethernet), a satellite network, a digital subscriber line (DSL) network, a cellular network, a Bluetooth connection, a near field communication (NFC) connection, etc. Some of the communications provided to the remote system may be associated with analysis results, imaging data, etc. generated or otherwise acquired by the system 900. Some of the communications provided to the system 900 may be associated with fluid analysis operations, patient records, and / or protocols performed by the system 900.

[0398] The one or more processors 994 and / or system 900 may include one or more of a processor-based system or a microprocessor-based system. In some implementations, the one or more processors 994 and / or system 900 include one or more of a programmable processor, a programmable controller, a microprocessor, a microcontroller, a graphics processing unit (GPU), a digital signal processor (DSP), a reduced instruction set computer (RISC), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device that performs various functions, including those described herein.

[0399] The memory 996 may include one or more of a semiconductor memory, a magnetically readable memory, an optical memory, a hard disk drive (HDD), an optical storage drive, a solid-state storage device, a solid-state drive (SSD), a flash memory, a read-only memory (ROM), an erasable programmable read-only memory (EPROM), an electrically erasable programmable read-only memory (EEPROM), a random access memory (RAM), a non-volatile RAM (NVRAM) memory, a compact disc (CD), a compact disc read-only memory (CD-ROM), a digital versatile disc (DVD), a Blu-ray® disc, a redundant array of independent disks (RAID) system, a cache, and / or any other storage device or storage disc in which information is stored for any duration (e.g., permanently, temporarily, long-term, for buffering, for caching).

[0400] The memory 996 may store instructions executable on the processor 994 that configure the sequencer communications module. The sequencer communications module may send and receive communications to the library preparation system via the communications interface 992, for example, using an Ethernet network. These communications may include information related to the library of samples. For example, the sequencer communications module may receive an indication of the preparation status of the library of samples from the library preparation system. The preparation status may indicate that the library preparation is complete and the library of samples is ready to be loaded onto the sequencer. The preparation status may also include an estimated duration until the library preparation is complete.

[0401] In another example, the sequencer communications module may receive, from the library preparation system, identification information (e.g., sample ID) for each sample in the library of samples. Further, for each sample, the sequencer communications module may receive, from the library preparation system, an indication of an index attached to the sample. In addition, the sequencer communications module may receive instructions from the library preparation system indicating the specific lane of the flow cell for each sample to be sequenced. The sequencer communications module may also receive one or more run parameters from the library preparation system such that the sequencer can sequence the library of samples using the received run parameters. The run parameters may include the number of cycles for each sample or any other suitable run parameters for sequencing.

[0402] Additionally, the sequencer communications module can send communications to the library preparation system. For example, the sequencer communications module can also send to the library preparation system sequencer status information, such as whether the sequencer is ready to receive a library of samples, an estimated duration until the sequencer can reach a safe pause point in the sequencing recipe that will not cause data quality issues for any runs that have already been performed and can receive a library of samples, an indication of completed sequencing setup steps, remaining sequencing setup steps, the expected duration of remaining sequencing steps, etc. The sequencer communications module can also send acknowledgments of communications sent by the library preparation system to the library preparation system. Furthermore, the sequencer communications module can send and receive any appropriate communications to and from the library preparation system associated with the library of samples.

[0403] 24B is a schematic diagram illustrating one implementation of a portion of a pump manifold assembly 986 for use with the system 900 of FIG. 24A. In the illustrated implementation, the pump manifold assembly 986 includes a body 832 that carries a pump valve 822, a cache valve 834, and a pump 821. The pump 821 may be a syringe pump and may be adapted to receive a volume of approximately 500 microliters (μL). Other volumes may prove suitable.

[0404] The sample loading assembly 938 defines pump ports 1005 (see FIG. 24A). Each pump port 1005 is coupled to a corresponding port 1007 of the pump manifold assembly 938 via a separate pump channel fluid line 830.

[0405] The pump valve 958, the cache valve 834, and / or the pump 821 are operable to individually control fluid flow to each channel 826 of the plurality of channels 826 of the flow cell 825. In the illustrated implementation, two pump drive assemblies 847 are provided. The pump drive assemblies 847 may be adapted to individually actuate one or more of the pumps 821 to perform one or more of the disclosed operations. In one implementation, one of the pump drive assemblies 847 may operate two of the pumps 821, and the other of the pump drive assemblies 847 may operate six of the pumps 821. Other arrangements may be identified as suitable.

[0406] The pump valve 958, the cache valve 834, and / or the pump 821 may be operable to flow one or more reagents through the bypass fluid line 962 and / or the main waste line 966. The body 832 of the pump manifold assembly 986 may also carry a plurality of sensors 836, 837. The sensors 836, 837 may include pressure sensors or flow sensors. Other types of sensors may prove suitable. In another implementation, one or more of the sensors 836, 837, and / or the cache valve 834 may be omitted. In some such implementations, the bypass fluid line 962 may also be omitted. Other arrangements may prove suitable.

[0407] The pump manifold assembly 986 includes a cache 960, pump channel fluid lines 830, a plurality of pump fluid lines 838, a shared fluid line 840, a cache fluid line 842, and a main waste line 966. The cache fluid line 842 is coupled to the cache 960 and the cache valve 834. The pump channel fluid lines 830 and the pump fluid lines 838 may be collectively referred to as pump channel fluid lines. In the illustrated implementation, each pump valve 822 is coupled to a corresponding pump channel fluid line 830, a corresponding pump fluid line 838, and a shared fluid line 840. Each pump 956 is coupled to a corresponding pump fluid line 838. The pump 821 is operable to individually control the flow of fluid to one of the pump channel fluid lines 830 and the channels 826 of the flow cell.

[0408] The cache valve 834 is coupled to a cache fluid line 842, a main waste line 966, and a shared fluid line 840. The sensors 836, 837 may be adapted to determine one or more of a pressure or flow value of at least one of the pump channel fluid lines 830 or one or more of the shared fluid lines 840. Five sensors 836 are coupled to the pump channel fluid lines 830. The sensors 836 may be arranged differently. Additional sensors or fewer sensors, including zero sensors, may prove suitable.

[0409] The pump valve 958, the cache valve 834, and / or the pump 956 may be operable to flow one or more reagents through the bypass fluid line 962 and / or the main waste line 966. The body 832 of the pump manifold assembly 938 may also carry a plurality of sensors 836, 837. The sensors 836, 837 may include pressure sensors or flow sensors. Other types of sensors may prove suitable. In another implementation, one or more of the sensors 836, 837, and / or the cache valve 834 may be omitted. In some such implementations, the bypass fluid line 962 may also be omitted. Other arrangements may prove suitable.

[0410] The pump manifold assembly 938 includes a cache 960, pump channel fluid lines 830, a plurality of pump fluid lines 838, a shared fluid line 840, a cache fluid line 8424, and a main waste line 966. The cache fluid line 8424 is coupled to the cache 960 and the cache valves 834. The pump channel fluid lines 830 and the pump fluid lines 838 may be collectively referred to as pump channel fluid lines. In the illustrated implementation, each pump valve 958 is coupled to a corresponding pump channel fluid line 830, a corresponding pump fluid line 838, and a shared fluid line 840. Each pump 956 is coupled to a corresponding pump fluid line 838. The pumps 956 are operable to individually control the flow of fluid to the pump channel fluid lines 830 and one of the channels 944 of the flow cell 906.

[0411] The cache valve 834 is coupled to the cache fluid line 8424, the main waste line 966, and the shared fluid line 840. The sensors 836, 837 may be adapted to determine one or more of a pressure or flow value of at least one of the pump channel fluid lines 830 or one or more of the shared fluid lines 840. Five sensors 836 are coupled to the pump channel fluid lines 830. The sensors 836 may be arranged differently. Additional sensors or fewer sensors, including zero sensors, may prove suitable.

[0412] To use one or more of the pumps 821 to draw fluid from or force fluid toward the flow cell 906, one or more of the pump valves 958 can be actuated to a first position that fluidly connects the pump channel fluid line 830 and the pump fluid line 838, while one or more of the pumps 821 can be actuated to move fluid.

[0413] To move reaction components toward the waste reservoir 817 using one or more of the pumps 821, one or more of the pump valves 958 may be actuated to a second position fluidically connecting the pump fluid line 838 with the shared fluid line 840, the cache valve 834 may be actuated to a first position fluidically connecting the shared fluid line 840 with the main waste line 966, and one or more of the pumps 821 may be actuated to move fluid.

[0414] To perform a mixing operation using one or more reaction components received through bypass fluid line 962, pump valve 958 may be actuated to a second position fluidly connecting pump fluid line 838 with shared fluid line 840, cache valve 834 may be actuated to a second position fluidly connecting cache fluid line 842 with shared fluid line 840, and one or more of pumps 821 may be actuated to move fluid. In some implementations, all of pumps 821 may be used to transfer a larger volume of reaction components through bypass fluid line 962 to prime shared fluid line 840. Then, to increase the accuracy of subsequent fluid transfers, for example, two of pumps 821 may be used while the remaining pumps 821 are idle. A different number of pumps 821 may be used instead, including using one pump 956.

[0415] 24C-24F illustrate a process for loading one or more target samples from a library preparation system and loading these target samples into a flow cell of a sequencing instrument. The library preparation system of FIGS. 24C-24F may be implemented by any of the disclosed examples, such as system 300 of FIG. 1. The sequencing instrument of FIGS. 24C-24F may be implemented by any of the disclosed examples, such as system 900 of FIG. 24A.

[0416] 24C illustrates the process of pump manifold assembly 936 priming fluid lines 188 and sample sipper assembly 174 of the library preparation system with liquid in the direction generally indicated by arrow 950. The liquid may be a buffer, and the buffer used to prime fluid lines 188 may be referred to as a read or read buffer.

[0417] 24D illustrates the process of the sample sipper assembly 174 drawing the target sample into the sequencing instrument in the direction generally indicated by arrow 952. In some examples, an air bubble may be placed between the buffer and the target sample.

[0418] 24E illustrates the process of the sample sipper assembly 174 drawing additional buffer into the sequencing instrument behind the target sample. The buffer behind the target sample may be referred to as a lag or lag buffer. An air bubble may, in some instances, be placed on either side of the target sample or between the buffer and the target sample.

[0419] 24F shows the process by which the pump manifold assembly 936 pushes the lag buffer, the sample of interest, and / or the read buffer into the flow cell 906. The lag buffer enters the flow cell 906 first in the illustrated embodiment.

[0420] 25 is a schematic diagram illustrating one implementation of the sipper assembly 174 of the first system 1000 and the second system 1002 carrying multiple flow cells 906. Each sipper 184 of the sipper assembly 174 is fluidly coupled to a corresponding channel 944 of the flow cell 906 by one of the fluid lines 188.

[0421] Each flow cell 906 has a pair of channels 944, a first channel opening 1004 located at a first end of each channel 944, and a second channel opening 1006 located at a second end of each channel 944. In the illustrated implementation, each pair of channels 944 shares a common second channel opening 1006. The first system 1000 may be a library preparation system such as systems 300, 400, 500, 600, 700, and 800 of FIGS. 1-23, and the second system 1002 may be a sequencing system such as system 900 of FIG. 24A. Thus, for example, a sample prepared by the first system 1000 may automatically flow from the first system 1000 to the second system 1002.

[0422] In other implementations, samples prepared by the first system 1000 can be automatically directed from the first system 1000 to the second system 1002 in a different manner. For example, the second system 1002 may be integrated into the first system 1000. As another example, samples prepared by the first system 1000 can be automatically loaded into a consumable (e.g., cartridge, flow cell), and the consumable can be automatically moved to and disposed within the second system 1002. In another example, a pipettor from either the first system 1000 or the second system 1002 can extend into the other system to aspirate and dispense samples. In another example, a shuttle can be positioned between the first system 1000 and the second system 1002 to transport samples between the two systems. In this example, samples can be loaded into sample-carrying containers, such as sample tubes or sample well plates, and placed on the shuttle to be transferred. The shuttle can also be used to transfer cartridges or flow cells. In another example, laboratory automation, such as via a truck, can be used to transfer samples in sample carriers, cartridges, or flow cells from the first system 1000 to the second system 1002.

[0423] FIG. 26 is a schematic diagram illustrating one implementation of another system 1000 that can be used to implement the system of FIG. 27-30 are diagrams illustrating a workflow that can be performed using the teachings of the present disclosure.

[0424] 31 is a schematic diagram illustrating one implementation of the sipper assembly 174 of the first system 1200 and the second system 1202 carrying multiple flow cells 906. Each sipper 184 of the sipper assembly 174 is fluidly coupled to a corresponding channel 944 of the flow cell 906 by one of the fluid lines 188.

[0425] Figure 32 is a diagram of another system 3300 that can be used to implement the system of Figure 1. The system 3200 shown is a library preparation system and includes a consumable area 3302, an assay bay 3304, a common bay 3306, a cross-bay gantry 3308, and a sample sipper assembly 3310. The assay bay 3304 may be referred to as the first work area, and / or the consumable area 3302 may be referred to as the consumable bay and / or the second work area. The sipper assembly 3310 may be omitted in other implementations.

[0426] The consumable area 3302 is shown carrying a plurality of well plates 3312, a plurality of assay bays 3304 each containing an assay bay plate receptacle 3314 and a pipette assembly 3316, a thermocycler 3318, and a magnet 3320 for performing amplification and cleanup processes associated with preparing a library of samples for sequencing. The well plates 3312 may be referred to as work plates. The assay bay plate receptacles 3314 may be referred to as plate receptacles. The common bay 3306 includes a common bay plate receptacle 3322 and an imaging system 3324 for performing quantification processes associated with preparing a library of samples for sequencing. The cross bay gantry 3308 includes a gripper 3326 that is movable between the consumable area 3302, the assay bays 3304, and the common bay 3306 during operation. The cross bay gantry 3308 is also shown to include a first contact dispenser 3327 and a second contact dispenser 3328. The sample sipper assembly 3310 has a plurality of shippers 3329 and an actuator 3330 for moving the shippers 3329 relative to the plate receptacle 3332. The sample sipper assembly 3310 is associated with transferring a library of samples to a sequencing system, such as the sequencing system 900 of Figure 24A. The fluid line 188 of Figure 1 and / or Figure 24 may be used to fluidly couple the shippers 3329 of the sample sipper assembly 3310 to the sequencing instrument.

[0427] A loading area 3334 is shown including the sample sipper assembly 3310 and a plate receptacle 3332. The loading area 3334 may include a stage 3336 for moving the plate receptacle 3332 relative to the sample sipper assembly 3310.

[0428] FIG. 33 is a plan view of the system 3200 of FIG. FIG. 34 is a front view of the system 3200 of FIG. Figure 35 is an isometric view of one of the assay bays 3304 of the system 3300 of Figure 32. The assay bay 3304 includes a pipette assembly 3316, a thermocycler 3318, a magnet 3320, and a drawer 3338 that is shown carrying different consumables 3340. The consumables 3340 may include liquid reagents, dry reagents, indexes, beads, well plates, waste, and / or pipette tips. The well plates may be referred to as work plates or plates. The waste may include liquid waste and / or tip waste. However, the drawer 3338 may carry additional or other consumables.

[0429] The pipette assembly 3316 is movable relative to the assay bay plate receptacle 3314 in the direction generally indicated by arrow 3342, allowing the pipette assembly 3316 to dispense and / or aspirate liquid from a well plate 3312, which is shown disposed on the assay bay plate receptacle 3314. The pipette assembly 3316 is movable relative to the assay bay plate receptacle 3314 in the direction generally indicated by arrow 3344, allowing the pipette assembly 3316 to dispense and / or aspirate liquid from a consumable 3340.

[0430] Figure 36 is a top view of the assay bay 3304 of Figure 35, including a pipette assembly 3316, a thermocycler 3318, a magnet 3320, and a drawer 3338, which are used to perform amplification and cleanup processes associated with preparing a library of samples for sequencing.

[0431] Figure 37 is an isometric view showing a portion of the exemplary pipette assembly 3316 of Figure 36. The pipette assembly 3316 includes a body 3346, a guide 3348, a bar 3350, a plurality of pipettes 3352, a plurality of gaskets 3354, and a pipette cam assembly 3356. The body 3346 includes a base 3358 that defines a pipette opening 3360, and the guide 3348 includes a protrusion 3362 that defines a pipette opening 3364 that aligns with the pipette opening 3360 in the base 3358. The bar 3350 includes a plurality of openings 3366, and the protrusion 3362 of the guide 3348 extends through the plurality of openings 3366 in the illustrated embodiment.

[0432] The pipettes 3352 are shown coupled to the body 3346 and extending through pipette openings 3360, 3364 in the body 3346 and the guide 3348. The pipettes 3352 each have an end 3368 that includes a flange 3370, and a gasket 3354 is disposed between the corresponding flange 3370 of the pipette 3352 and the protrusion 3362.

[0433] In operation, the pipette cam assembly 3356 moves the body 3346 away from the guide 3348 and moves the flange 3370 of the pipette 3352 toward the protrusion 3362 to compress the gasket 3354, and moves the body 3346 toward the guide 3348 and moves the flange 3370 of the pipette 3352 away from the protrusion 3362 to relax the gasket 3354. When the end 3368 of the pipette 3352 is positioned within the pipette tip 3372, the gasket 3354 is compressed, allowing the gasket to form a bond with the pipette tip 3372. When the end 3368 of the pipette 3352 is positioned within the pipette tip 3372, the gasket 3354 is relaxed, allowing the pipette tip 3372 to disengage from the pipette 3352.

[0434] The guide 3348 includes an outward channel 3374, and the bar 3350 includes a first arm 3376 and a second arm 3378 that extend into the outward channel 3374 of the guide 3348. The first arm 3376 and the second arm 3378 can interact with a surface of the guide 3348 to guide movement of the first arm 3376 and the second arm 3378 generally in the direction indicated by the arrow 3380.

[0435] Shown is a pipette assembly 3316 including a guide bearing 3382, a bar bearing 3384, and a camshaft 3386. The guide bearing 3382 is coupled to the guide 3348, and the bar bearing 3384 is coupled to corresponding first and second arms 3376 and 3378 of the bar 3350. The camshaft 3386 includes an inner lobe 3388 and an outer lobe 3390, where the inner lobe 3388 engages the guide bearing 3382 and the outer lobe 3390 engages the bar bearing 3384. The inner lobe 3388 of the camshaft 3386 engaging the guide bearing 3382 moves the body 3346 away from the guide 3348 and moves the flange 3370 of the pipette 3352 toward the protrusion 3362, compressing the gasket 3354 during operation. The inner lobe 3388 of the camshaft 3386 engaging the guide bearing 3382 in the second position allows the body 3346 to move toward the guide 3348, moving the flange 3370 of the pipette 3352 away from the protrusion 3362 and relaxing the gasket 3354 during operation. A compressed gasket 3354 allows the gasket to form a bond with the pipette tip 3372, and a relaxed gasket 3354 allows the pipette tip 3372 to not be bonded to the pipette 3352.

[0436] The outer lobe 3390 of the camshaft 3386 engaging the bar bearing 3384 moves the bar 3350 toward the flange 3370 of the pipette 3352, engaging the pipette tip 3372 with the bar 3350 and urging the pipette tip 3372 to be released from the pipette assembly 3316. In the illustrated implementation, one of the bar bearings 3384 faces one of the guide bearings 3382. However, the bearings 3382, 3384 may be positioned differently.

[0437] 38 is an isometric view of the pipette assembly 3316 of FIG. 37 with the guide 3348 removed. The pipette assembly 3316 may include a vertical guide 3391 coupled to the body 3346 and including a stop 3392. The vertical guide 3391 may be threadably engaged with the body 3346 of the pipette assembly 3316, and the stop 3392 may, for example, limit the movement of the bar 3350 toward the body 3346. The guide 3348 may define a guide opening through which the vertical guide 3391 passes. The vertical guide 3391 and the surfaces of the guide 3348 that define the guide opening may guide movement of the guide 3348 in the direction generally indicated by the arrow 3380. FIG. 39 is a front cross-sectional view of the pipette assembly 3316 of FIG. 38. A torsion bar spring 3393 is shown disposed between the rod 3350 and the guide 3348, and a guide spring 3394 is shown disposed between the body 3346 and the guide 3348. The torsion bar spring 3393 biases the bar bearing 3384 toward the corresponding outer lobe 3390, and the guide spring 3394 biases the body 3346 away from the guide 3348.

[0438] 38 , the body 3346 has a first side 3396 and a second side 3398, and the camshaft 3386 has a first camshaft portion 3400 and a second camshaft portion 3402. The first camshaft portion 3400 is coupled to the first side 3396 of the body 3346, and the second camshaft portion 3402 is coupled to the second side 3398 of the body 3346. The first camshaft portion 3400 is spaced apart from the second camshaft portion 3402 in the illustrated implementation. For example, the pipette 3352 is shown disposed between the first camshaft portion 3400 and the second camshaft portion 3402.

[0439] Shown is a pipette assembly 3316 including a motor 3404 and a gear set 3406. The motor 3404 is carried by the pipette assembly 3316 and may be coupled to the body 3346, for example. The gear set 3406 is coupled to a camshaft 3386. Movement of the motor 3404 rotates the camshaft 3386 during operation. The motor 3404 is shown positioned to rotate the gear set 3406, which rotates the camshaft 3386.

[0440] The gear set 3406 includes first and second gears 3408, 3410, first and second pinions 3412, 3414, and a shaft 3416 that couples the first and second pinions 3412, 3414. Thus, when the shaft 3416 rotates, both the first and second pinions 3412, 3414 rotate. The motor gear 3418 is coupled to the motor 3404 and meshes with the first gear 3408. The first gear 3408 meshes with the first pinion 3412, and the second pinion 3414 meshes with the second gear 3410. The first gear 3408 is coupled to a first side 3396 of the body 3346 and the inner lobe 3388 and outer lobe 3390 on the first side 3396 of the body 3346, and the second gear 3410 is coupled to a second side 3398 of the body 3346 and the inner lobe 3388 and outer lobe 3390 on the second side 3398 of the body 3346.

[0441] During operation, the motor 3404 rotates the motor gear 3418, and engagement between the motor gear 3418 and the first gear 3408 rotates the first pinion 3412, which in turn rotates the first camshaft portion 3400. Rotation of the first pinion 3412 rotates the shaft 3416, which in turn rotates the second pinion 3414. Rotation of the second pinion 3414 rotates the second gear 3410 and the second camshaft portion 3402.

[0442] The first side 3396 and the second side 3398 of the body 3346 define a shaft opening 3420, and the shaft 3416 is rotatably coupled within the shaft opening 3420. The shaft 3416 is spaced from the pipette 3352.

[0443] Figure 40 is a rear cross-sectional view of the pipette assembly 3316 of Figure 38. The body 3346 has a first side 3396, a second side 3398, and a wall 3442 that define a receptacle 3444. The pipettes 3352 are disposed within the receptacle 3444. Each pipette 3352 has a barrel 3446 with a piston 3448 disposed within and movable within the corresponding barrel 3446.

[0444] An actuator 3450 is coupled to the piston 3448 to move the piston 3448 between a retracted position and an extended position within the barrel 3446. The actuator 3450, in the illustrated implementation, includes a ball screw 3452. The actuator 3450 may also include a pair of linear rails 3454 and a lift 3456. The lift 3456 is coupled to the piston 3448 and the linear rail 3454 and, in the illustrated implementation, is movable by the ball screw 3452. The lift 3456 is C-shaped 3458 and has an end 3460. A carriage 3462 is coupled to the corresponding end 3460 of the lift 3456 and is coupled to the linear rail 3454.

[0445] 41 is a front view of the pipette assembly 3316 of FIG. 42 is a side view of the pipette assembly 3316 of FIG. 38 showing the end 3368 of the pipette 3352 inserted into the pipette tip 3372. FIG.

[0446] Figure 43 is a side view of the pipette assembly 3316 of Figure 38, showing the camshaft 3386 rotated 90 degrees relative to the position of the camshaft 3386 in Figure 42. The gasket 3354 is compressed to form a bond with the pipette tip 3372 in the position shown. The pipette assembly 3316, in the illustrated implementation, can compress the gasket 3354 in a repeatable manner to ensure that the pipette tip 3371 is secured to the pipette assembly 3316 in the same or a substantially similar position. Having the pipette tip 3371 in a known, repeatable position allows for more reagent to be withdrawn from the reagent well and / or reduces dead volume.

[0447] Figure 44 is a side view of the pipette assembly 3316 of Figure 38, showing the camshaft 3386 rotated 90 degrees relative to the position of the camshaft 3386 in Figure 43. The gasket 3354 relaxes, allowing the pipette tip 3372 to be separated from the end 3368 of the pipette 3352.

[0448] Figure 45 is a side view of the pipette assembly 3316 of Figure 38, showing the camshaft 3386 rotated 90 degrees relative to the position of the camshaft 3386 in Figure 44. The gasket 3354 relaxes and the bar 3350 is moved generally in the direction indicated by arrow 3466, pushing the pipette tip 3372 out of the pipette 3352.

[0449] Figure 46 is an isometric view of one thermocycler 3318 of the assay bay 3304 of Figure 32. The thermocycler 3318 includes a base 3468, a plate receptacle 3314, and a cover assembly 3470. The base 3468 includes a stop wall 3472, the plate receptacle 3314 is disposed on the base 3468, and the cover assembly 3470 is movably coupled to the base 3468.

[0450] The cover assembly 3470 includes a sled 3474, a cover 3476, a cover follower 3478, and a cam assembly 3480. The sled 3474 has a front wall 3482 and a rear wall 3484, with a receptacle 3486 defined between the front wall 3482 and the rear wall 3484. The cover 3476 is disposed within the receptacle 3486 of the sled 3474, and the cover follower is disposed within the receptacle 3486 of the sled 3474 and is movably coupled to the cover 3476.

[0451] In operation, the cam assembly 3480 moves the cover 3476 toward the base 3468 to cover the plate receptacle 3314 and moves the cover follower 3478 toward the base 3468. The plate receptacle 3314 is shown to receive a plate 3488 having wells 3490, and the thermocycler 3318 can regulate the temperature of samples in the wells 3490 of the plate 3488 during operation.

[0452] Figure 47 is an enlarged isometric view of the thermocycler 3318 of Figure 46. The cam assembly 3480 is shown to include an inner cam plate 3492, an outer cam plate 3494, a cover bearing 3495, an inner slot bearing 3496, a cover follower bearing 3498, and an outer slot bearing 3500. The inner cam plates 3492 are coupled to the sleds 3474 and each define an inner cam slot 3502, and the outer cam plates 3494 are coupled to the base 3468 and each define an outer cam slot 3504.

[0453] The cover bearing 3495 is coupled to the cover 3476 and positioned to engage the stop wall 3472, the inner slot bearing 3496 is coupled to the cover 3476 and movably positioned within the inner cam slot 3502. The cover follower bearing 3498 is coupled to the cover 3476 and positioned to engage the rear wall 3484 of the sled 3474, and the outer slot bearing 350 is coupled to the cover follower 3478 and movably positioned within the outer cam slot 3504.

[0454] The cover bearing 3495 engages the stop wall 3472 during operation, causing the inner slot bearing 3496 to move within the inner cam slot 3502 and the cover bearing 3495 to move along the stop wall 3472, thereby moving the cover 3476 toward the base 3468 in the direction generally indicated by arrow 3506, covering the plate receptacle 3314. The cover follower bearing 3498 engages the rear wall 3484 during operation, causing the outer slot bearing 3500 to move within the outer cam slot 3504 and the cover follower bearing 3498 to move along the rear wall 3484, causing the cover follower 3478 to move toward the base 3468 in the direction generally indicated by arrow 3506. A spring 3508 is included that biases the cover 3476 away from the cover follower 3478. The spring 3508 may be a coil spring or another biasing element.

[0455] Figure 48 is an isometric view of the thermocycler 3318 of Figure 46 , omitting the inner cam plate 3492, outer cam plate 3494, sled 3474, and spring 3508. Shown is a guide rod 3510 that movably couples the cover 3476 and the cover follower 3478. The cover 3476 has a blind hole 3512, and the cover follower 3478 has a through hole 3514. The guide rod 3510 is disposed within the corresponding blind hole 3512 in the cover 3476 and the through hole 3514 in the cover follower 3478. The spring 3508 surrounds the corresponding guide rod 3510.

[0456] The cover 3476 defines a cover bearing receptacle 3516 in which the cover bearing 3495 is disposed, and the cover follower 3478 defines a cover follower bearing receptacle 3518 in which the cover follower bearing 3498 is disposed. A linear rail 3520 is coupled to the base 3468, and a carriage 3522 is coupled to the rear wall 3484 and to the linear rail 3520.

[0457] 46 , the stop wall 3472 has extensions 3524 defining an opening 3526 therebetween. The front wall 3482 is sized to pass between the extensions 3524, and the cover bearing 3495 engages the extensions. An actuator 3528 and magnet 3320 may be included, where the actuator 3528 moves the magnet 3320 relative to the plate receptacle 3314. The thermocycler 3318 may be used during the amplification process, and the magnet 3320 and / or actuator 3528 may be used during the cleanup process.

[0458] 49 is a side view of the thermocycler 3318 with the cover assembly 3470 in the rear position, not covering the plate 3488. The spring 3508 is shown in the extended position.

[0459] 50 is a side view of the thermocycler 3318 with the cover assembly 3470 in a forward, lowered position, covering the plate 3488. The spring 3508 is shown in a compressed position.

[0460] Figure 51 is an isometric view of one drawer 3338 of the assay bay 3304 of Figure 32. The drawer 3338 includes a platform 3529, a plate receptacle 3530, a small liquid reagent well plate receptacle 3532, a large liquid reagent well plate receptacle 3534, a dry well plate receptacle 3536, and a waste reservoir 3538. The plate receptacle 3530, the small liquid reagent well plate receptacle 3532, and the large liquid reagent well plate receptacle 3534 are coupled to the platform 3529, and the dry well plate receptacle 3536 is disposed on the platform 3529.

[0461] The small liquid reagent well plate receptacle 3532 has a base 3540, a first end wall 3542, and a second end wall 3544. The first end wall 3542 is coupled to the base 3540 and has an inwardly extending lip 3546 which forms a first groove 3547 with the base 3540, and the second end wall 3544 is coupled to the base 3540 and has an inwardly extending lip 3548 which forms a second groove 3549 and includes a key 3550. The large liquid reagent well plate receptacle 3534 is also coupled to the platform 3529 and includes a base 3540, a first end wall 3542, and a second end wall 3544. The first end wall 3542 has an inwardly extending lip 3546 that forms a first groove 3547 with the base of the large liquid reagent well plate receptacle 3534, and the second end wall 3544 has an inwardly extending lip 3548 that forms a second groove 3549 with the base of the large liquid reagent well plate receptacle 3534 and includes a key 3550. The consumable 3340 forms a snap-fit ​​connection with the first groove 3547 and the second groove 3549, and the key 3550 provides a fool-proof mechanism to allow the consumable 3340 to be mated with the small liquid reagent well plate receptacle 3532 and the large liquid reagent well plate receptacle 3534 in a specific orientation.

[0462] The dry-well plate receptacle 3536 is disposed on the platform 3529 and defines a waste reservoir compartment 3552. The waste reservoir 3538 has a wide portion 3554 that includes an inlet 3556 and a narrow portion 3558 extending from the wide portion 3554 and shown disposed within the waste reservoir compartment 3552. However, the dry-well plate receptacle 3536 and / or the waste reservoir compartment 3552 may be configured differently. The waste reservoir 3538 can receive pipette tips 3372 and / or liquid waste. The inlet 3556 is, for example, a rectangular inlet 3557 for receiving waste associated with a multi-tip pipette, such as the pipette assembly 3316. However, the inlet 3556 may be a different shape.

[0463] A central well plate support wall 3560 extends from the base 3540 and is disposed between a first end wall 3542 and a second end wall 3544 of the small liquid reagent well plate receptacle 3532. The small liquid reagent well receptacle 3532, in the illustrated implementation, includes two central well plate support walls 3560. The central well plate support wall 3562 extends from the base 3540 and is disposed between a first end wall 3542 and a second end wall 3544 of the large liquid reagent well plate receptacle 3534. The large liquid reagent well receptacle 3534, in the illustrated implementation, includes two central well plate support walls 3562. The height of the support walls 3560, 3562 corresponds to the height of the corresponding consumable 3340 / well plate. The support walls 3560, 3562 can, for example, support the corresponding consumable 3340 and / or encourage the top surface of the consumable 3340 to be substantially flat and / or prevent the top surface of the consumable 3340 from becoming concave.

[0464] The small liquid reagent well plate receptacle 3532, in the illustrated implementation, is positioned between the plate receptacle 3530 and the large liquid reagent well plate receptacle 353. The large liquid reagent well plate receptacle 3534, in the illustrated implementation, is positioned between the small liquid reagent well plate receptacle 3532 and the dry well plate receptacle 3536. The dry well plate receptacle 3536, in the illustrated implementation, is positioned between the large liquid reagent well plate receptacle 3534 and the wide portion 3554 of the waste reservoir 3538, which includes an inlet 3556. The reagent well plate receptacles 3532 and / or 3534 and / or the dry well plate receptacle 3536 may be in different locations and / or may be omitted.

[0465] The drawer 3338 also, in the illustrated implementation, includes a tip receptacle 3564. The tip receptacle 3564 is located between the large liquid reagent well plate receptacle 3534 and the dry well plate receptacle 3536. However, the tip receptacle 3564 may be in another location.

[0466] FIG. 52 is an isometric view of the drawer 3338 of FIG. 51 with the consumables 3340 removed, but including the dry well plate receptacle 3536 and waste reservoir 3538.

[0467] FIG. 53 is an isometric view of the drawer 3338 of FIG. 51 with the consumables 3340 and dry well plate receptacle 3536 removed. FIG. 54 is a top view of the drawer 3338 of FIG. 51, which includes a consumable 3340, a dry well plate receptacle 3536, and a waste reservoir 3538.

[0468] FIG. 55 is a side view of the drawer 3338 of FIG. 51, which includes a consumable 3340, a dry well plate receptacle 3536, and a waste reservoir 3538. FIG. 56 is an isometric view of a reagent well plate 3566 including a first end wall 3568, a second end wall 3570, and a panel 3572 that can be used with the system 3300 of FIG. 32 . The reagent well plate 3566 of FIG. 56 is a small liquid reagent well plate 3573 in the illustrated embodiment. The first end wall 3568 has a male snap-fit ​​component 3574, and the second end wall 3570 has a male snap-fit ​​component 3574. The first end wall 3568 and the second end wall 3570 each have two male snap-fit ​​components in the illustrated implementation. The panel 3572 is coupled to and extends between the first end wall 3568 and the second end wall 3570, defines a reagent well receptacle 3576, and includes a top surface 3578. A reagent well 3580 is disposed within the reagent well receptacle 3576. The reagent well 3580 has an end 3582 with an annular collar 3584 that is shown engaging the top surface 3578 of the panel 3572 .

[0469] The first end wall 3568, in the illustrated implementation, has a keying notch 3586. The keying notch 3586 can receive the keys 3550 of the small and large liquid reagent well plate receptacles 3532, 3534 to provide a foolproof mechanism for allowing the consumable 3340 to be mated with the small and large liquid reagent well plate receptacles 3532, 3534 in a particular orientation.

[0470] An impermeable barrier 3588 is coupled to the edge 3582 of the reagent well 3580. The impermeable barrier 3588 may comprise foil and / or plastic. The impermeable barrier 3588 is shown as a single sheet coupled to the edge 3582 of the reagent well 3580. Alternatively, individual impermeable barriers 3588 may be coupled to each of the reagent wells 3580, as shown, for example, in FIG. 63. A machine-readable code 3590 is also included. The machine-readable code 3590 may be coupled to the impermeable barrier 3588, as shown in the implementation of FIG. 56. The machine-readable code 3590 may additionally or alternatively be coupled to the panel 3572 and / or the end walls 3568 and / or 3570.

[0471] Figure 57 is a side view of the reagent well plate 3566 of Figure 56. The first end wall 3568 and the second end wall 3570 extend outward from a panel 3572, which may be concave in the illustrated implementation. The panel 3572 may alternatively have a different shape and / or may not be concave. The panel 3572 may be substantially flat when the first end wall 3568 and the second end wall 3570 are coupled to the reagent well plate receptacles 3532 and / or 3534. The first end wall 3568 and the second end wall 3570 may be substantially parallel to one another and / or may have a smaller outward tapered shape, for example, when the first end wall 3568 and the second end wall 3570 are coupled to the reagent well plate receptacles 3532 and / or 3534.

[0472] Figure 58 is an isometric view of one of the reagent wells 3580 of the reagent well plate 3566 of Figure 56. The reagent well 3580, in the illustrated implementation, has a second annular collar 3592 that is longitudinally spaced from the annular collar 3584. When the reagent well 3580 is received in the reagent well receptacle 3576 and the reagent well 3580 is coupled to the panel 3572, the panel 3572 is disposed between the annular collar 3584 of the reagent well 3580 and the second annular collar 3592.

[0473] Figure 59 is an isometric view of another reagent well plate 3594 including a first end wall 3568, a second end wall 3570, and a panel 3572. The reagent well plate 3594, in the illustrated implementation, is a large liquid reagent well plate 3956. The reagent wells 3580 in Figure 59 are shown as being longer and / or larger than the reagent wells 3580 in Figure 58. The panel 3572 of the reagent well plate 3594 in Figure 56 has a plurality of second reagent well receptacles 3958 having a different size than the reagent well receptacles 3576. The second reagent well receptacles 3958 are disposed between the second end wall 3570 and the reagent well receptacles 3576 in the illustrated implementation.

[0474] The bulk reagent wells 3960 are disposed within the second reagent well receptacle 3958. An L-tab 3962 is coupled to each of the bulk reagent wells 3960. The L-tab 3962 has a first leg 3964 coupled to the bulk reagent well 3960 and a second leg 3966 extending from the first leg 3964 at an angle corresponding to the angle of the second end wall 3570. The second leg 3966 is shown extending along the second end wall 3570. The L-tab 3962 is disposed within the dimensional envelope of the reagent well plate 3566 in the illustrated implementation.

[0475] Figure 60 is a side view of the reagent well plate 3594 of Figure 59. The second end wall 3570 includes a first wall section 3968 and a second wall section 3970 joined to one another to form a recess 3971. The L-tab 3962 is positioned within the dimensional envelope of the recess 3971, as shown in Figure 59.

[0476] FIG. 61 is a side view of the bulk reagent well 3960 of FIG. Figure 62 is an isometric view of the bulk reagent well 3960 of Figure 60. A machine readable code 3590 is shown on the first leg 3964 of the L-tab 3962. The machine readable code 3590 can include information about the reagent contained within the bulk reagent well 3960, such as the type of reagent, the date of manufacture, etc.

[0477] Figure 63 is an isometric view of another reagent well plate 3972 that includes a first end wall 3568, a second end wall 3570, and a panel 3572 that can be used with the system of Figure 32. The reagent well plate 3972, in the illustrated implementation, is a dry reagent well plate 3974.

[0478] In the illustrated implementation, the first end wall 3568 has a pair of first end wall portions 3976 and a pair of male snap-fit ​​components 3574, and the second end wall 3570 includes a pair of second end wall portions 3978 and a pair of male snap-fit ​​components 3574. Each of the first end wall portions 3976 includes one of the male snap-fit ​​components 3574, and each of the second end wall portions 3978 includes one of the male snap-fit ​​components 3574. The male snap-fit ​​components 3574 each have a tapered tab 3980. However, the male snap-fit ​​components 3574 may be alternatively configured.

[0479] The male snap-fit ​​connection 3574 may form a snap-fit ​​connection with, for example, a dry well plate receptacle 3536. A plurality of impermeable barriers 3588 are shown, with each reagent well 3580 covered by one of the impermeable barriers 3588.

[0480] FIG. 64 is a side view of the reagent well plate 3594 of FIG. Figure 65 is an isometric view of a reagent well 3580 of the reagent well plate 3594 of Figure 63. The impermeable barrier 3588 includes indicia 3982. The indicia 3982 may include a machine-readable code and / or indicator of the reagent contained within the reagent well 3580.

[0481] Figure 66 is an isometric view of a well plate 3312 that can be used with the system 3300 of Figure 32. The well plate 3312 includes a rectangular wall 3984 and a panel 3986 coupled to the rectangular wall 3984. The rectangular wall 3984 has an end wall 3988 and a side wall 3990. The end wall 3988 and the side wall 3990 extend outwardly from the panel 3986. The end wall 3988 each has a notch 3992 and a recess 3994 that form a handle 3996 that extends between the side walls 3990. A gripper 3326 can interact with the handle 3996 to move the well plate 3312 between the consumable area 3302, the assay bays 3304, and / or the common bay 3306. For example, the gripper 3326 may have an extension that can be inserted into the notch 3992 to lift and / or hold the well plate 3312. The extension may extend inward.

[0482] The panel 3986 defines the reagent well receptacles 3576 and includes a top surface 3578. The panel 3986, in the illustrated implementation, has multiple rows of the reagent well receptacles 3576. Alternatively, the panel 3986 can have a single row of reagent well receptacles 3576 or more than two rows of reagent well receptacles 3576.

[0483] The reagent well 3580 includes an end 3582 having an annular collar 3584. The reagent well 3580 is disposed within the reagent well receptacle 3576, with the annular collar 3584 shown engaging the top surface 3578.

[0484] The end wall 3988, including the handle 3996, in the illustrated implementation forms a dogbone shape 3998. The rectangular wall 3984 and the panel 3986 form a step 4000, and the rectangular wall 3984 has an end 4002 that forms an opening 4004 sized to receive the step 4000 of an adjacent well plate 3312, as shown in FIG.

[0485] Figure 67 is an isometric view of the stack of well plates 3312 of Figure 66. The cutouts 3992 and recesses 3994 in adjacent well plates are shown forming openings 4008. The openings 4008 may be sized to allow a gripper 3326 to access the openings 4008 and, for example, lift one or more of the top well plates 3312 from the stack of well plates 3312.

[0486] FIG. 68 is a cross-sectional end view of the stack of well plates 3312 of FIG. FIG. 69 is a top view of the well plate 3312 of FIG. FIG. 70 is a side view of the well plate of FIG.

[0487] Figure 71 is an isometric view of another stack of well plates 4010 that can be used with the system 3300 of Figure 32. The well plate 4010 is similar to the well plate 3312 of Figure 66, but includes a single row of reagent well receptacles 3576.

[0488] FIG. 72 is a bottom isometric view of the well plate 4010 of FIG. FIG. 73 is a cross-sectional end view of the stack of well plates 4010 of FIG. Figure 74 is an isometric view of a stack of lids 4012 that can be used to cover the well plate 3312 of Figure 66. The lid 4012 has a lid rectangular wall 4014 and a lid panel 4016. The lid panel 4016 has two rows of receptacles 4017 configured to cover two rows of reagent wells 3580.

[0489] The lid rectangular wall 4014 has lid end walls 4018 and lid side walls 4020. The lid end walls 4018 each include a lid notch 4022 that extends between the lid side walls 4020 and forms a handle 4024. The lid notches 4022 of adjacent lids 4012 form an opening 4026.

[0490] The lid rectangular wall 4014 and the lid panel 4016 form a lid step 4028, and the lid rectangular wall 4014 has an end 4030 that forms a lid opening 4032 sized to receive the lid step 4028 of the adjacent lid 4012.

[0491] Figure 75 is an isometric view of a lid 4034 that can be used to cover the well plate 4010 of Figure 71. The lid 4034 is similar to the lid 4012 of Figure 74, except that the panel 4016 has receptacles 4036 configured to cover a single row of reagent wells 3580.

[0492] 76 is a top view of an exemplary sample cartridge 5000 including multiple wells 5002 that can be used with any of the disclosed implementations. The sample cartridge 5000 can be used, by way of example, with the sample sipper assembly 3310 of the system 3300 of FIG. 32. The wells 5002 can, in some implementations, include pool wells, prime wells, and / or wash wells.

[0493] 77 is a top view of an exemplary reagent cartridge 5004 including multiple wells 5002 that may be used with any of the disclosed implementations. The reagent cartridge 5004 may be used, by way of example, with the common bay 3306 of the system 3300 of FIG. 32. The reagent cartridge 5004 may contain reagents such as those used during a quantification process, a denaturation process, and / or a dilution process.

[0494] Figure 78 is a plan view of an exemplary system 5050 that can be used to implement the system 300 of Figure 1. The system 5050 of Figure 78 includes four assay bays 3304, a common bay 3306, and a shipper assembly 3310.

[0495] FIG. 79 is a front isometric view of one implementation of the system 5050 of FIG. Figure 80 is a rear isometric view of one implementation of the system 5050 of Figure 78. The grippers 3326 of the cross bay gantry 3308 are shown including extensions 5052. The extensions 5052 are movable toward and / or away from each other to move the consumables 3340 between, by way of example, the consumable area 3302, the assay bay 3304, and / or the common bay 3306. The grippers 3326, the first contact dispenser 3327, and the second contact dispenser 3328 are shown carried by the cross bay gantry 3308.

[0496] Figure 81 is an isometric view of one of the assay bays 3304 of the system 5050 of Figure 79. The Figure 81 assay bay 3304 is similar to the assay bay 3304 of Figure 35. However, the assay bay 3304 of Figure 81 includes a drawer 5054 in which the consumables 3340 are arranged differently.

[0497] Figure 82 is an isometric view of the assay bay 3304 of Figure 81 with the drawer 5054 partially removed. The waste reservoir 3538 is shown extending through the platform 3529 of the drawer 5054.

[0498] Figure 83 is an isometric view of one exemplary implementation of an assay bay 3304 including an alternative pipette assembly 5056 that may be used to implement the system 300 of Figure 1 and / or the system 3300 of Figure 32. The pipette assembly 5056 may include an xyz stage 5058 that moves the shipper 3329 relative to the well plates 3312 disposed on the assay bay plate receptacles 3314 and / or relative to the consumables 3340 disposed on the drawers 5060 of the assay bay 3304. In the illustrated implementation, the pipette 5056 is shown including four tips, and each column of the well plates 3312 includes 12 wells.

[0499] The pipette assembly 5056 may use a first set of tips to perform a process associated with a first group of wells of the well plate 3312, and the pipette assembly 5056 may use a second set of tips to perform a process associated with a second group of wells of the well plate 3312. The stage 5058 may move the tips of the pipette assembly 5056 between the first and second groups of wells in the direction generally indicated by arrow 5062. The pipette assembly 5056 may temporarily store the first set of tips when performing a process associated with the second group of wells, and / or the pipette assembly 5056 may temporarily store the second set of tips when performing a process associated with the first group of wells.

[0500] FIG. 84 is a side view of the drawer 5060 of the assay bay 3304 of FIG. Figure 85 is a plan view of an exemplary system 5100 that can be used to implement the imaging system 300 of Figure 1. The system 5100 of Figure 83 includes a consumable area 3302, two assay bays 3304, a common bay 3306, and a shipper assembly 3310.

[0501] Example 1. A modular system for preparing a library of samples for sequencing, the modular system comprising: a first assay bay for performing a first assay, the first assay bay comprising: a first contact dispenser; a first work area, the first work area comprising a work plate receptacle, a thermocycler, and a magnet; a first drawer, the first drawer comprising a consumable area adapted to receive a work plate adapted to contain a sample and a plurality of consumables for interacting with the sample; a common bay, the common bay comprising an analyzer area including an imaging system; and a mover operably coupled to the first assay bay and the common bay, the mover the mover is movable in a first direction along the first assay bay and in a second direction perpendicular to the first direction between the first assay bay and the common bay, the mover is configured to move a working plate from the consumable area to a working plate receptacle in the first working area; the first contact dispenser is linearly movable in the first direction between the consumable area and the first working area and is configured to move a working plate in the consumable area to a working plate in the first working area and move a plurality of consumables between the consumable area and the working plate in the first working area; and the mover is further configured to move a sample from the first working area to the analyzer area for analysis by the imaging system.

[0502] Example 2. The modular system of Example 1, wherein the first contact dispenser is not movable in the second direction. Example 3. The modular system of example 1 or 2, wherein the first contact dispenser and the mover are both movable in a third direction perpendicular to the first and second directions.

[0503] Example 4. The modular system of any one of Examples 1-3, wherein the common bay further comprises a pooling area, and the mover is configured to move between the analyzer area and the pooling area.

[0504] Example 5. The modular system of any one of Examples 1-4, wherein the first contact dispenser comprises a first contact head configured to hold a tip. Example 6. The modular system of any one of Examples 1-5, wherein the first drawer is linearly movable in a first direction relative to the first work area between a loading position and an operating position, and wherein when the first drawer is in the loading position, the first drawer is spaced a first distance from the first work area, and when the first drawer is in the operating position, the first drawer is spaced a second distance from the first work area, the second distance being less than the first distance.

[0505] Example 7. The modular system of any one of Examples 1-6, further comprising a movable stage coupled to the first contact dispenser for linearly moving the first contact dispenser in the first direction and the third direction.

[0506] Example 8. The modular system of Example 7, further comprising a first actuator operably coupled to the movable stage and the magnet, the first actuator configured to actuate movement of the movable stage to move the magnet relative to the work plate receptacle.

[0507] Example 9. The modular system of any one of Examples 1-8, further comprising a gantry system, wherein the mover is movable along the gantry system. Example 10. The modular system of any one of Examples 1-9, further comprising a second actuator configured to actuate movement of the mover in the first direction and the second direction.

[0508] Example 11. The modular system of any one of Examples 1-10, further comprising a door movable to enclose the thermocycler and work plate receptacle. Example 12. The modular system of any one of Examples 1-11, wherein the thermocycler is aligned with the work plate receptacle in a first orientation.

[0509] Example 13. The modular system of any one of Examples 1-12, wherein the thermocycler is configured to amplify samples in a working plate. Example 14. The modular system of any one of Examples 1-13, wherein the consumable area is adapted to receive a lid for the work plate, and the first contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

[0510] Example 15. The modular system of any one of Examples 1 to 14, wherein the plurality of consumables includes a tip tray including a first reusable tip and a second reusable tip, one or more additional work plates, an index tray adapted to accommodate indexes, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate reagents.

[0511] Example 16. The modular system of Example 15, wherein the first contact dispenser is configured to use a first reusable tip to transfer beads in the consumable area to a work plate in the first work area and to use a second reusable tip to transfer one or more reagents from a reagent reservoir in the consumable area to the work plate.

[0512] Example 17. The modular system of Example 15, wherein the first contact dispenser is configured to use the first reusable tip to transfer beads in the consumable area to a work plate in the first work area, and to use the first reusable tip to transfer one or more reagents from a reagent reservoir in the consumable area to the work plate.

[0513] Example 18. The modular system of any one of Examples 15-17, wherein the first contact dispenser is configured to aspirate an index from an index tray in the consumable area and dispense the index into a work plate in the first work area.

[0514] Example 19. The modular system of any one of Examples 15-18, wherein the first contact dispenser is configured to aspirate beads from a bead tray in the consumable area and dispense the beads into a work plate in the first work area.

[0515] Example 20. The modular system of Example 19, wherein the magnet is movable toward the work plate receptacle to attract beads in the work plate toward the magnet, and the first contact dispenser is configured to aspirate a first reagent from a reagent reservoir in the consumable area and dispense the first reagent into the work plate.

[0516] Example 21. The modular system of Example 20, wherein the first contact dispenser is configured to aspirate the sample and the first reagent from the work plate, the mover is configured to move the work plate to the consumable area and move a second work plate of the one or more additional work plates in the consumable area to a work plate receptacle in the first work area, the first contact dispenser is configured to dispense the sample and the first reagent into the second work plate, and the mover is configured to move the second work plate from the first work area to the analyzer area.

[0517] Example 22. The modular system of any one of Examples 1-21, wherein the imaging system is configured to acquire image data of the first reagent and a portion of the sample to determine a concentration of the sample.

[0518] Example 23. A second assay bay arranged parallel to the first assay bay, the second assay bay for performing a second assay, further comprising: a second contact dispenser; a second work area comprising a work plate receptacle, a thermocycler, and a magnet; and a second drawer comprising a consumable area adapted to receive a work plate adapted to contain a sample, and a plurality of consumables for interacting with the sample; and a mover operably coupled to the second assay bay for moving the work plate to the second consumable area. the second contact dispenser is configured to move a plurality of consumables between the consumable area and a working plate in a working plate receptacle in the second working area; the second contact dispenser is movable linearly in a first direction between the consumable area and the second working area; the second contact dispenser is configured to move a plurality of consumables between the consumable area and a working plate in a working plate receptacle in the second working area; the mover is movable in a second direction between the second assay bay and the common bay; and the mover is configured to move a sample from the second working area to the analyzer area for analysis by the imaging system.

[0519] Example 24. The modular system of Example 23, wherein the second assay is run simultaneously with the first assay. Example 25. A system comprising: the modular system of any one of Examples 1-24; a sequencer; and a plurality of fluid lines fluidly coupling the common bay and the sequencer such that prepared samples automatically flow from the common bay to the sequencer.

[0520] Example 26. The system of Example 25, wherein the common bay comprises a sipper assembly having a plurality of sippers, the sequencer comprises a plurality of flow cells, and the plurality of fluid lines fluidly couple the plurality of sipper with the plurality of flow cells.

[0521] Example 27. A modular bay for preparing a library of samples for sequencing, comprising: a contact dispenser; a work area comprising a work plate receptacle, a thermocycler, and a magnet; a drawer comprising a consumable area adapted to receive a work plate adapted to contain a sample, and a plurality of consumables for interacting with the sample; wherein the contact dispenser is linearly movable longitudinally between the consumable area and the work area, whereby the contact dispenser is configured to move the plurality of consumables between the consumable area and the work plate in the work area.

[0522] Example 28. The modular bay of example 26 or 27, wherein the contact dispenser comprises a contact head configured to hold a tip. Example 29. The modular bay of example 27 or 28, wherein the drawer is movable linearly longitudinally relative to the work area between a loading position and an operating position, and wherein when the drawer is in the loading position, the drawer is spaced a first distance from the work area, and when the drawer is in the operating position, the drawer is spaced a second distance from the work area, the second distance being less than the first distance.

[0523] Example 30. The modular bay of any one of Examples 27-29, wherein the contact dispenser is not movable laterally perpendicular to the longitudinal direction. Example 31. The modular bay of any one of Examples 27-30, further comprising a movable stage operably coupled to the contact dispenser for linearly moving the contact dispenser longitudinally.

[0524] Example 32. The modular bay of example 31, further comprising an actuator configured to actuate movement of the movable stage in the longitudinal direction. Example 33. The modular bay of any one of Examples 27-32, further comprising a door movable to enclose the thermocycler and work plate receptacle.

[0525] Example 34. The modular bay of any one of Examples 27-33, wherein the thermocycler is longitudinally aligned with the work plate receptacle. Example 35. The modular bay of any one of Examples 27-34, wherein the thermocycler is configured to amplify samples in a working plate.

[0526] Example 36. The modular bay of any one of Examples 27-35, wherein the consumable area is adapted to receive a lid for the work plate, and the first contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

[0527] Example 37. The modular bay described in any one of Examples 27 to 36, wherein the plurality of consumables includes a tip tray including a first reusable tip and a second reusable tip, one or more additional work plates, an index tray adapted to accommodate indexes, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate reagents.

[0528] Example 38. The modular bay of Example 37, wherein the contact dispenser is configured to use a first reusable tip to transfer beads from a bead tray in the consumable area to a work plate in the first work area and to use a second reusable tip to transfer one or more reagents from a reagent reservoir in the consumable area to the work plate.

[0529] Example 39. The modular bay of example 37 or 38, wherein the first contact dispenser is configured to aspirate an index from an index tray in the consumable area and dispense the index into a work plate in the work area.

[0530] Example 40. The modular bay of any one of Examples 37-39, wherein the contact dispenser is configured to aspirate beads from a bead tray in the consumable area and dispense the beads into a work plate in the work area.

[0531] Example 41. The modular bay of Example 40, wherein the magnet is movable toward the work plate receptacle to attract beads in the work plate toward the magnet, and the contact dispenser is configured to aspirate a first reagent from a reagent reservoir in the consumable area and dispense the first reagent into the work plate.

[0532] Example 42. The modular bay of Example 41, wherein the contact dispenser is configured to aspirate the sample and the first reagent from the work plate, and the contact dispenser is configured to dispense the sample and the first reagent into a second work plate of the one or more additional work plates in the consumable area.

[0533] Example 43. An apparatus comprising: a chip tray including a first chip and a second chip; a consumable area including a consumable receptacle that receives a first plate having wells for containing samples; a second plate having wells; an index tray having wells for containing indexes; and a bead tray having wells for containing beads; a mover; a contact dispenser; a stage that moves the contact dispenser; a plate receptacle; a magnet; a thermocycler; and an analyzer area including an imaging system.

[0534] Example 44. The apparatus of example 43, further comprising an actuator that moves the magnet relative to the plate receptacle. Example 45. The apparatus of any one of Examples 43-44, wherein the thermocycler is aligned with the plate receptacle.

[0535] Example 46. The apparatus of any one of Examples 43-45, wherein the mover moves the first plate from the consumable area to the plate receptacle. Example 47. The apparatus of Example 46, wherein the stage aligns the contact dispenser with the chip tray, and the contact dispenser couples with a first chip from the chip tray, the stage aligns the contact dispenser with an index tray, and the contact dispenser aspirates an index from the index tray, and the stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses the index into a well of the first plate.

[0536] Example 48. The apparatus of Example 47, wherein the thermocycler amplifies samples in the wells of the first plate. Example 49. The apparatus of any one of Examples 43-48, wherein the consumable area further comprises a lid, and the mover moves the lid from the consumable area and places the lid on the first plate to cover the wells of the first plate.

[0537] Example 50. The apparatus of any one of Examples 43-49, wherein the mover moves the lid from the first plate to the consumable area. Example 51. An apparatus described in any one of Examples 49-50, wherein the stage aligns the contact dispenser with a bead tray, and the contact dispenser aspirates beads from the bead tray, and the stage aligns the contact dispenser with a first plate, and the contact dispenser dispenses beads into wells of the first plate.

[0538] Example 52. The apparatus of Example 16, wherein the stage aligns the contact dispenser with the first plate, and the contact dispenser dispenses the first reagent into the wells of the first plate.

[0539] Example 53. The apparatus of Example 52, wherein the stage aligns the contact dispenser with the chip tray, the contact dispenser places a first chip into the chip tray, and the contact dispenser couples with a second chip from the chip tray.

[0540] Example 54. The apparatus of any one of Examples 52-53, wherein the actuator moves the magnet toward the plate receptacle to attract beads toward the magnet, and the stage aligns the contact dispenser with the first plate to enable the contact dispenser to aspirate the first reagent from the wells.

[0541] Example 55. The apparatus of Example 54, wherein the system includes a waste material and the contact dispenser dispenses the first reagent into the waste material. Example 56. The apparatus of Example 55, wherein the stage aligns the contact dispenser with the first plate, and the contact dispenser dispenses the second reagent into the wells of the first plate.

[0542] Example 57. The apparatus of Example 56, wherein the actuator moves the magnet toward the plate receptacle to attract beads toward the magnet, the stage aligns the contact dispenser with the first plate to enable the contact dispenser to aspirate the second reagent and sample from the wells of the first plate, and the stage aligns the contact dispenser with the second plate to enable the contact dispenser to dispense the second reagent and sample into the wells of the second plate.

[0543] Example 58. The apparatus of Example 57, wherein the imaging system acquires image data of the second reagent and a portion of the sample, and the system determines the concentration of the sample. Example 59. The device of example 58, further comprising a second contact dispenser.

[0544] Example 60. The apparatus of Example 59, wherein the stage aligns a second plate with a second contact dispenser, and the second contact dispenser dispenses a diluent into the wells of the second plate to dilute the sample based on the determined concentration of the sample.

[0545] Example 61. The apparatus of any one of Examples 43-60, wherein the system includes a first work area including a contact dispenser, a stage for moving the contact dispenser, a plate receptacle, a magnet, and a thermocycler.

[0546] Example 62. The apparatus of any one of Examples 43-61, wherein the system comprises a second work area comprising a mover, a second contact dispenser, a plate receptacle, and an analyzer comprising an imaging system.

[0547] Example 63. The system of any one of Examples 43-62, wherein the system comprises a loading area. Example 64. The apparatus of example 63, wherein the loading area comprises a shipper assembly.

[0548] Example 65. The apparatus of example 64, wherein the sipper assembly comprises a sample sipper assembly. Example 66. The device of any one of Examples 63-64, wherein the loading area comprises a plate receptacle.

[0549] Example 67. The apparatus of example 66, wherein the loading area comprises a stage for moving the plate receptacle relative to the shipper assembly. Example 68. The apparatus of any one of Examples 43-67, further comprising a second system.

[0550] Example 69. The apparatus of example 68, wherein a second system is fluidly coupled to the system. Example 70. The apparatus of any one of Examples 68-69, wherein the second system comprises a sequencing instrument.

[0551] Example 71. The apparatus of any one of Examples 43 to 70, wherein the thermocycler is positioned below the plate receptacle. Example 72. The apparatus of any one of Examples 43-71, wherein the plate receptacle includes a heat block defining a well receptacle, and the thermocycler is positioned below the well receptacle.

[0552] Example 73. The apparatus of any one of Examples 43-72, further comprising a heat sink coupled to the thermocycler. Example 74. The apparatus of any one of Examples 43-72, further comprising a lid and an actuator, the actuator configured to move the lid relative to the plate receptacle to cover the plate receptacle.

[0553] Example 75. An apparatus comprising a library preparation system and a sequencing system fluidly coupled to the library preparation system. Example 76. An apparatus comprising a system including a bay, a consumable area including a consumable receptacle, a first contact dispenser, a stage for moving the first contact dispenser, a work area including a first working plate receptacle, a magnet, and a thermocycler, a second work area including a second plate receptacle, and an analyzer area including an imaging system, a second contact dispenser, a second stage for moving the second contact dispenser relative to the first bay and the second work area, and a mover.

[0554] Example 77. A modular system for preparing a library of samples for sequencing, the modular system comprising: a first assay bay, the first contact dispenser; a first work area, the first work area comprising a work plate receptacle, a thermocycler, and a magnet; a first drawer, the first drawer comprising a consumable area adapted to receive a sample plate adapted to contain a sample and a plurality of consumables for interacting with the sample; a common bay, the common bay comprising an analyzer area including an imaging system; and a common bay operably coupled to the first assay bay and the common bay. a mover configured to move a first contact dispenser linearly in a first direction between the consumable area and the first work area, whereby the first contact dispenser is configured to (i) move a sample plate in the consumable area to a work plate in the first work area, and (ii) move a plurality of consumables between the consumable area and the sample plate in the first work area; and a mover configured to move a first contact dispenser linearly in a first direction between the consumable area and the first work area, whereby the first contact dispenser is configured to (i) move a sample plate in the consumable area to a work plate in the first work area, and (ii) move a plurality of consumables between the consumable area and the sample plate in the first work area, and the mover is movable between the first assay bay and a common bay in the first direction and in a second direction perpendicular to the first direction, whereby the mover is configured to move the sample plate from the first work area to the analyzer area for analysis by the imaging system.

[0555] Example 78. A modular bay for preparing a library of samples for sequencing, comprising: a contact dispenser; a work area comprising a work plate receptacle, a thermocycler, and a magnet; a drawer comprising a consumable area adapted to receive a work plate adapted to contain a sample; and a plurality of consumables for interacting with the sample, wherein the contact dispenser is linearly movable longitudinally between the consumable area and the work area, whereby the contact dispenser is configured to (i) move a sample plate in the consumable area to a work plate in the work area, and (ii) move the plurality of consumables.

[0556] Example 79. An apparatus comprising a pipette assembly comprising: a body having a base defining a plurality of pipette openings; a guide having a plurality of protrusions defining pipette openings that align with the pipette openings of the base; a bar having a plurality of openings through which the protrusions of the guide extend; a plurality of pipettes coupled to the body and extending through the pipette openings of the body and guide, each pipette having an end with a flange; a plurality of gaskets disposed between the flanges and the protrusions of a corresponding pipette; and a pipette cam assembly for moving the body away from the guide and moving the flanges of the pipettes towards the protrusions to compress the gaskets, and for moving the body towards the guide and moving the flanges of the pipettes away from the protrusions to relax the gaskets.

[0557] Example 80. The device of example 79, wherein the gasket is compressed when the end of the pipette is placed into the pipette tip, allowing the gasket to form a bond with the pipette tip.

[0558] Example 81. The device of any one of Examples 79-80, wherein the gasket is relaxed when the end of the pipette is placed in the pipette tip, allowing the pipette tip to be uncoupled from the pipette.

[0559] Example 82. The device of any one of Examples 79-81, wherein the guide comprises an outward channel and the bar comprises a first arm and a second arm extending into the outward channel of the guide. Example 83. The apparatus of any one of Examples 79 to 81, wherein the bar comprises a first arm and a second arm, and the pipette cam assembly comprises a guide bearing coupled to the guide, a bar bearing coupled to the corresponding first arm and second arm, and a cam shaft including an inner lobe that engages the guide bearing and an outer lobe that engages the bar bearing.

[0560] Example 84. The device of example 83, wherein engagement of the inner lobe of the camshaft with the guide bearing moves the body away from the guide and moves the flange of the pipette toward the protrusion to compress the gasket.

[0561] Example 85. The device of any one of Examples 83-84, wherein the inner lobe of the camshaft engaging the guide bearing in the second position allows the guide to move toward the bar and move the flange of the pipette away from the protrusion, relaxing the gasket.

[0562] Example 86. The apparatus of any one of Examples 83-85, wherein engagement of the outer lobe of the camshaft with the rod bearing moves the bar toward a flange of the pipette, allowing the bar to engage a pipette tip carried by the pipette and bias the pipette tip such that the pipette tip is released from the pipette assembly.

[0563] Example 87. The apparatus of any one of Examples 83 to 86, wherein one of the bar bearings faces one of the guide bearings. Example 88. The apparatus of any one of Examples 83-87, further comprising a torsion bar spring disposed between the bar and the guide to bias the bar bearing toward the corresponding outer lobe.

[0564] Example 89. The device of any one of Examples 79-88, further comprising a guide spring disposed between the body and the guide to bias the body away from the guide. Example 90. The apparatus of any one of Examples 83-89, wherein the body comprises a first side and a second side, the camshaft comprises a first camshaft portion and a second camshaft portion, the first camshaft portion coupled to the first side of the body, and the second camshaft portion coupled to the second side of the body.

[0565] Example 91. The apparatus of example 90, wherein the first camshaft portion is spaced apart from the second camshaft portion. Example 92. The apparatus of any one of Examples 83-91, further comprising a motor and a gear set, the gear set being coupled to the camshaft.

[0566] Example 93. The device of example 92, wherein movement of the motor rotates the camshaft. Example 94. The apparatus of any one of Examples 92-93, wherein the gear set comprises first and second gears, first and second pinions, and a shaft connecting the first and second pinions.

[0567] Example 95. The apparatus of Example 94, wherein the body comprises a first side and a second side, the first gear is coupled to the first side of the body and to inner and outer lobes on the first side of the body, and the second gear is coupled to the second side of the body and to inner and outer lobes on the second side of the body.

[0568] Example 96. The device of Example 95, wherein the first side and the second side of the body define a shaft opening, and the shaft is rotatably coupled within the shaft opening. Example 97. The device of example 96, wherein the shaft is spaced from the pipette.

[0569] Example 98. The device of any one of Examples 79 to 97, wherein the body comprises a first side and a second side and a wall defining a receptacle, and the pipette is disposed within the receptacle. Example 99. The device of any one of Examples 79-98, wherein the pipettes each comprise a barrel, and the device further comprises a plurality of pistons disposed within and movable within the corresponding barrels.

[0570] Example 100. The apparatus of example 99, further comprising an actuator coupled to the piston to move the piston between a retracted position and an extended position within the barrel. Example 101. The device of example 100, wherein the actuator includes a ball screw.

[0571] Example 102. The apparatus of example 101, wherein the actuator comprises a pair of linear rails and a lift, the lift being coupled to the piston and the linear rail and movable by a ball screw.

[0572] Example 103. The apparatus of example 102, wherein the lift is C-shaped and has ends, and the apparatus further comprises a carriage coupled to a corresponding end of the lift and coupled to the linear rail. Example 104. An apparatus including a thermocycler, the thermocycler comprising: a base including a stop wall; a plate receptacle on the base; and a cover assembly movably coupled to the base, the cover assembly comprising: a sled having a base including a stop wall; a plate receptacle on the base; a front wall; a rear wall; and a receptacle defined between the front and rear walls; a cover disposed within the receptacle on the sled; a cover follower disposed within the receptacle on the sled and movably coupled to the cover; and a cam assembly for moving the cover toward the base to cover the plate receptacle and for moving the cover follower toward the base, wherein the plate receptacle receives a plate having wells, and the thermocycler regulates the temperature of samples in the wells of the plate.

[0573] Example 105. The apparatus of example 104, wherein the cam assembly includes inner cam plates coupled to the sled, each defining an inner cam slot, outer cam plates coupled to the base, each defining an outer cam slot, a cover bearing coupled to the cover and positioned to engage the stop wall, an inner slot bearing coupled to the cover and movably positioned within the inner cam slot, a cover follower bearing coupled to the cover follower and positioned to engage a rear wall of the sled, and an outer slot bearing coupled to the cover follower and movably positioned within the outer cam slot.

[0574] Example 106. The apparatus of example 105, wherein the cover bearing engages the stop wall and moves the inner slot bearing within the inner cam slot, causing the cover bearing to move along the stop wall and move the cover toward the base to cover the plate receptacle.

[0575] Example 107. The apparatus of any one of Examples 105-106, wherein the cover follower bearing engages the rear wall and moves the outer slot bearing within the outer cam slot, causing the cover follower bearing to move along the rear wall and move the cover follower toward the base.

[0576] Example 108. The device of any one of Examples 104 to 107, further comprising a spring biasing the cover away from the cover follower. Example 109. The device of any one of Examples 104-108, further comprising a guide rod movably coupling the cover and the cover follower.

[0577] Example 110. The apparatus of example 109, wherein the cover includes a blind hole, the cover follower includes a through hole, and the guide rod is disposed within the corresponding blind hole in the cover and the through hole in the cover follower.

[0578] Example 111. The device of any one of Examples 109-110, wherein the spring surrounds a corresponding guide rod. Example 112. The apparatus of any one of Examples 105-111, wherein the cover defines a cover bearing receptacle in which the cover bearing is disposed.

[0579] Example 113. The apparatus of any one of Examples 105-112, wherein the cover follower defines a cover follower bearing receptacle in which the cover follower bearing is disposed. Example 114. The apparatus of any one of Examples 104-113, further comprising a linear rail coupled to the base and a carriage coupled to the rear wall and coupled to the linear rail.

[0580] Example 115. The device of any one of Examples 104-114, wherein the stop wall comprises extensions having an opening defined therebetween, and the front wall is sized to pass between the extensions.

[0581] Example 116. The device of example 115, wherein the cover bearing engages the extension. Example 117. The device of any one of Examples 104-116, further comprising a magnet and an actuator, the actuator moving the magnet relative to the plate receptacle.

[0582] Example 118. An apparatus comprising a drawer with a platform, the drawer comprising: a plate receptacle coupled to the platform; a small liquid reagent well plate receptacle coupled to the platform, the small liquid reagent well plate receptacle comprising a base and a first end wall having an inwardly extending lip forming a first groove with the base, and a second end wall coupled to the base and having an inwardly extending lip forming a second groove with the base, the second end wall comprising a key; and a large liquid reagent well plate receptacle coupled to the platform, the large liquid reagent well plate receptacle comprising a base and a first end wall having an inwardly extending lip forming a second groove with the base, the second end wall comprising a key. an apparatus comprising: a large liquid reagent well plate receptacle having a first end wall with an inwardly extending lip that forms a first groove with the base of the large liquid reagent well plate receptacle; and a second end wall that is coupled to the base and has an inwardly extending lip that forms a second groove with the base of the large liquid reagent well plate receptacle, the second end wall having a key; a dry well plate receptacle positioned on a platform and defining a waste reservoir compartment; and a waste reservoir having a wide portion including an inlet and a narrow portion extending from the wide portion and positioned within the waste reservoir compartment.

[0583] Example 119. The apparatus of Example 118, further comprising a central well plate support wall extending from the base and positioned between the first end wall and the second end wall of the compact liquid reagent well plate receptacle.

[0584] Example 120. The apparatus of any one of Examples 118-119, further comprising a central well plate support wall extending from the base and positioned between the first end wall and the second end wall of the large liquid reagent well plate receptacle.

[0585] Example 121...

Claims

1. 1. A modular system for preparing a library of samples for sequencing, said modular system comprising: a first assay bay for conducting a first assay, a first contact dispenser; a first work area, Work plate receptacle, Thermocyclers, and magnet, a first work area comprising: a first drawer comprising a consumable area adapted to receive a working plate adapted to contain samples and a plurality of consumables for interacting with the samples; a first assay bay comprising: a common bay, the common bay comprising an analyzer area including an imaging system; a mover operably coupled to the first assay bay and the common bay; Equipped with the mover is movable in a first direction along the first assay bay and in a second direction perpendicular to the first direction between the first assay bay and the common bay, and is configured to move the working plate from the consumable area to the working plate receptacle in the first work area; the first contact dispenser is linearly movable in the first direction between the consumable area and the first work area, and the first contact dispenser is configured to move the plurality of consumables between the consumable area and the work plate in the work plate receptacle in the first work area; The mover is further configured to move the sample from the first work area to the analyzer area for analysis by the imaging system.

2. The modular system of claim 1 , wherein the first contact dispenser is not movable in the second direction.

3. 3. The modular system of claim 1 or 2, wherein the first contact dispenser and the mover are both movable in a third direction perpendicular to the first direction and the second direction.

4. The modular system of any one of claims 1 to 3, wherein the common bay further comprises a pooling area, and the mover is configured to move between the analyzer area and the pooling area.

5. The modular system of any one of claims 1 to 4, wherein the first contact dispenser comprises a first contact head configured to hold a tip.

6. 6. The modular system of claim 1, wherein the first drawer is linearly movable in the first direction relative to the first work area between a loading position and an operating position, and when the first drawer is in the loading position, the first drawer is spaced a first distance from the first work area, and when the first drawer is in the operating position, the first drawer is spaced a second distance from the first work area, the second distance being smaller than the first distance.

7. 7. The modular system of claim 1, further comprising a movable stage coupled to the first contact dispenser for linearly moving the first contact dispenser in the first direction and the third direction.

8. 8. The modular system of claim 7, further comprising a first actuator operably coupled to the movable stage and the magnet, the first actuator configured to actuate movement of the movable stage to move the magnet relative to the work plate receptacle.

9. The modular system of any one of claims 1 to 8, further comprising a gantry system, the mover being movable along the gantry system.

10. The modular system of any one of claims 1 to 9, further comprising a second actuator configured to actuate movement of the mover in the first direction and in the second direction.

11. The modular system of any one of claims 1 to 10, further comprising a door movable to enclose the thermocycler and the work plate receptacle.

12. The modular system of any one of claims 1 to 11, wherein the thermocycler is aligned with the work plate receptacle in the first orientation.

13. The modular system of any one of claims 1 to 12, wherein the thermocycler is configured to amplify the samples in the working plate.

14. 14. The modular system of claim 1, wherein the consumable area is adapted to receive a lid for the work plate, and the first contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

15. 15. The modular system of claim 1, wherein the plurality of consumables include a tip tray including a first reusable tip and a second reusable tip, one or more additional work plates, an index tray adapted to accommodate an index, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate a reagent.

16. 16. The modular system of claim 15, wherein the first contact dispenser is configured to use the first reusable tip to transfer the beads in the consumable area to the work plate in the first work area and to use the second reusable tip to transfer one or more reagents from the reagent reservoirs in the consumable area to the work plate.

17. 16. The modular system of claim 15, wherein the first contact dispenser is configured to use the first reusable tip to transfer the beads in the consumable area to the work plate in the first work area, and to use the first reusable tip to transfer one or more reagents from the reagent reservoirs in the consumable area to the work plate.

18. 18. The modular system of claim 15, wherein the first contact dispenser is configured to aspirate the index from the index tray in the consumable area and dispense the index into the work plate in the first work area.

19. 19. The modular system of claim 15, wherein the first contact dispenser is configured to aspirate the beads from the bead tray in the consumable area and dispense the beads into the work plate in the first work area.

20. 20. The modular system of claim 19, wherein the magnet is movable toward the work plate receptacle to attract the beads in the work plate toward the magnet, and the first contact dispenser is configured to aspirate a first reagent from the reagent reservoir in the consumable area and dispense the first reagent into the work plate.

21. 21. The modular system of claim 20, wherein the first contact dispenser is configured to aspirate the sample and the first reagent from the working plate, the mover is configured to move the working plate to the consumable area and move a second working plate of the one or more additional working plates in the consumable area to the working plate receptacle in the first working area, the first contact dispenser is configured to dispense the sample and the first reagent into the second working plate, and the mover is configured to move the second working plate from the first working area to the analyzer area.

22. 22. The modular system of claim 1, wherein the imaging system is configured to acquire image data of the first reagent and the portion of the sample to determine a concentration of the sample.

23. a second assay bay disposed parallel to the first assay bay, the second assay bay for conducting a second assay; a second contact dispenser; a second work area, Work plate receptacle, Thermocyclers, and magnet, a second work area comprising: a second drawer comprising a consumable area adapted to receive a working plate adapted to contain samples and a plurality of consumables for interacting with the samples; a second assay bay comprising: the mover is operably coupled to the second assay bay and configured to move the working plate from the second consumable area to the working plate receptacle in the second work area; the second contact dispenser is linearly movable in the first direction between the consumable area and the second work area, and the second contact dispenser is configured to move the plurality of consumables between the consumable area and the work plate in the work plate receptacle in the second work area; 23. The modular system of claim 1, wherein the mover is movable in the second direction between the second assay bay and the common bay, and the mover is configured to move the sample from the second working area to the analyzer area for analysis by the imaging system.

24. 24. The modular system of claim 23, wherein the second assay is performed simultaneously with the first assay.

25. A modular system according to any one of claims 1 to 24; A sequencer, a plurality of fluid lines fluidly coupling the common bay and the sequencer such that the prepared samples automatically flow from the common bay to the sequencer; A system comprising:

26. 26. The system of claim 25, wherein the common bay comprises a sipper assembly having a plurality of sipper, the sequencer comprises a plurality of flow cells, and the plurality of fluid lines fluidly couple the plurality of sipper with the plurality of flow cells.

27. A modular bay for preparing a library of samples for sequencing, comprising: a contact dispenser; A work area, Work plate receptacle, Thermocyclers, and magnet, a work area comprising: a drawer comprising a consumable area adapted to receive a working plate adapted to contain samples and a plurality of consumables for interacting with the samples; Equipped with The contact dispenser is movable linearly longitudinally between the consumable area and the work area, and the contact dispenser is configured to move the plurality of consumables between the consumable area and the work plate within the work area.

28. 28. The modular bay of claim 26 or 27, wherein the contact dispenser comprises a contact head configured to hold a tip.

29. 29. A modular bay as described in claim 27 or 28, wherein the drawer is movable linearly in the longitudinal direction relative to the work area between a loading position and an operating position, and when the drawer is in the loading position, the drawer is spaced a first distance from the work area, and when the drawer is in the operating position, the drawer is spaced a second distance from the work area, the second distance being smaller than the first distance.

30. A modular bay according to any one of claims 27 to 29, wherein the contact dispenser is not movable laterally perpendicular to the longitudinal direction.

31. The modular bay of any one of claims 27 to 30, further comprising a movable stage operatively coupled to the contact dispenser for linearly moving the contact dispenser in the longitudinal direction.

32. 32. The modular bay of claim 31, further comprising an actuator configured to actuate movement of the movable stage in the longitudinal direction.

33. A modular bay according to any one of claims 27 to 32, further comprising a door movable to enclose the thermocycler and the work plate receptacle.

34. A modular bay according to any one of claims 27 to 33, wherein the thermocycler is aligned in the longitudinal direction with the work plate receptacle.

35. A modular bay according to any one of claims 27 to 34, wherein the thermocycler is configured to amplify the samples in the working plate.

36. 36. The modular bay of claim 27, wherein the consumable area is adapted to receive a lid for the work plate, and the first contact dispenser is configured to move the lid from the consumable area and place the lid on the work plate.

37. 37. The modular bay of claim 27, wherein the plurality of consumables include a tip tray including a first reusable tip and a second reusable tip, one or more additional work plates, an index tray adapted to accommodate indexes, a bead tray adapted to accommodate beads, and a reagent reservoir adapted to accommodate a reagent.

38. 38. The modular bay of claim 37, wherein the contact dispenser is configured to use the first reusable tip to transfer the beads from the bead tray in the consumable area to the work plate in the first work area and to use the second reusable tip to transfer one or more reagents from the reagent reservoir in the consumable area to the work plate.

39. 39. The modular bay of claim 37 or 38, wherein the first contact dispenser is configured to aspirate the index from the index tray in the consumable area and dispense the index into the work plate in the work area.

40. 40. The modular bay of any one of claims 37 to 39, wherein the contact dispenser is configured to aspirate the beads from the bead tray in the consumable area and dispense the beads into the work plate in the work area.

41. 41. The modular bay of claim 40, wherein the magnet is movable toward the work plate receptacle to attract the beads in the work plate toward the magnet, and the contact dispenser is configured to aspirate a first reagent from the reagent reservoir in the consumable area and dispense the first reagent into the work plate.

42. 42. The modular bay of claim 41, wherein the contact dispenser is configured to aspirate the sample and the first reagent from the work plate, and the contact dispenser is configured to dispense the sample and the first reagent into a second of the one or more additional work plates in the consumable area.

43. 1. An apparatus comprising:

1. A system comprising: a consumables area, a consumable receptacle that receives a chip tray including a first chip and a second chip, a first plate having wells for accommodating samples, a second plate having wells, an index tray having wells for accommodating indexes, and a bead tray having wells for accommodating beads; a consumables area including With Mova, a contact dispenser; a stage for moving the contact dispenser; a plate receptacle; A magnet and A thermocycler and an analyzer area equipped with an imaging system; A system comprising: An apparatus comprising:

44. 44. The apparatus of claim 43, further comprising an actuator for moving the magnet relative to the plate receptacle.

45. 45. The apparatus of any one of claims 43 to 44, wherein the thermocycler is aligned with the plate receptacle.

46. The apparatus of any one of claims 43 to 45, wherein the mover moves the first plate from the consumable area to the plate receptacle.

47. 47. The apparatus of claim 46, wherein the stage aligns the contact dispenser with the chip tray, the contact dispenser combines with the first chip from the chip tray, the stage aligns the contact dispenser with the index tray, the contact dispenser aspirates the index from the index tray, and the stage aligns the contact dispenser with the first plate, the contact dispenser dispenses the index into the well of the first plate.

48. 48. The apparatus of claim 47, wherein the thermocycler amplifies the samples in the wells of the first plate.

49. 49. The apparatus of any one of claims 43 to 48, wherein the consumable area further comprises a lid, and wherein the mover moves the lid from the consumable area and places the lid on the first plate to cover the wells of the first plate.

50. The apparatus of any one of claims 43 to 49, wherein the mover moves the lid from the first plate to the consumable area.

51. The apparatus of any one of claims 49 to 50, wherein the stage aligns the contact dispenser with the bead tray, the contact dispenser aspirating the beads from the bead tray, and the stage aligns the contact dispenser with the first plate, the contact dispenser dispensing the beads into the wells of the first plate.

52. 17. The apparatus of claim 16, wherein the stage aligns the contact dispenser with the first plate, and the contact dispenser dispenses a first reagent into the wells of the first plate.

53. 53. The apparatus of claim 52, wherein the stage aligns the contact dispenser with the chip tray, the contact dispenser places the first chip into the chip tray, and the contact dispenser mates with the second chip from the chip tray.

54. 54. The apparatus of any one of claims 52 to 53, wherein the actuator moves the magnet toward the plate receptacle to attract the beads toward the magnet, and the stage aligns the contact dispenser with the first plate to enable the contact dispenser to aspirate the first reagent from the wells.

55. 55. The apparatus of claim 54, wherein the system includes a waste product, and the contact dispenser dispenses the first reagent into the waste product.

56. 56. The apparatus of claim 55, wherein the stage aligns the contact dispenser with the first plate, and the contact dispenser dispenses a second reagent into the wells of the first plate.

57. 57. The apparatus of claim 56, wherein the actuator moves the magnet toward the plate receptacle to attract the beads toward the magnet, the stage aligns the contact dispenser with the first plate to enable the contact dispenser to aspirate the second reagent and the sample from the wells of the first plate, and the stage aligns the contact dispenser with the second plate to enable the contact dispenser to dispense the second reagent and the sample into the wells of the second plate.

58. 58. The apparatus of claim 57, wherein the imaging system acquires image data of the second reagent and a portion of the sample, and the system determines a concentration of the sample.

59. 59. The device of claim 58, further comprising a second contact dispenser.

60. 60. The apparatus of claim 59, wherein the stage aligns the second plate with the second contact dispenser, and the second contact dispenser dispenses a diluent into the wells of the second plate to dilute the sample based on the determined concentration of the sample.

61. 61. The apparatus of any one of claims 43 to 60, wherein the system includes a first working area including the contact dispenser, the stage for moving the contact dispenser, the plate receptacle, the magnet, and the thermocycler.

62. 62. The apparatus of any one of claims 43 to 61, wherein the system comprises a second work area comprising the mover, a second contact dispenser, a plate receptacle, and an analyzer comprising an imaging system.

63. A system according to any one of claims 43 to 62, wherein the system comprises a loading area.

64. 64. The apparatus of claim 63, wherein the loading area comprises a shipper assembly.

65. 65. The apparatus of claim 64, wherein the sipper assembly comprises a sample sipper assembly.

66. 65. Apparatus according to any one of claims 63 to 64, wherein the loading area comprises a plate receptacle.

67. 67. The apparatus of claim 66, wherein the loading area comprises a stage for moving the plate receptacle relative to the shipper assembly.

68. 68. Apparatus according to any one of claims 43 to 67, further comprising a second system.

69. 69. The apparatus of claim 68, wherein the second system is fluidly coupled to the system.

70. 70. The apparatus of any one of claims 68 to 69, wherein the second system comprises a sequencing instrument.

71. 71. The apparatus of any one of claims 43 to 70, wherein the thermocycler is located below the plate receptacle.

72. 72. The apparatus of any one of claims 43 to 71, wherein the plate receptacle includes a heat block defining a well receptacle, and the thermocycler is positioned below the well receptacle.

73. 73. The apparatus of any one of claims 43 to 72, further comprising a heat sink coupled to the thermocycler.

74. 73. The apparatus of any one of claims 43 to 72, further comprising a lid and an actuator, the actuator moving the lid relative to the plate receptacle to cover the plate receptacle.

75. 1. An apparatus comprising: Library preparation systems, and a sequencing system fluidly coupled to the library preparation system.

76. 1. An apparatus comprising:

1. A system comprising: It is a bay, a consumable area including a consumable receptacle; a first contact dispenser; a stage for moving the first contact dispenser; A work area, a first plate receptacle; Magnets, and Thermocycler a work area comprising: a bay comprising: a second work area comprising a second plate receptacle and an analyzer area comprising an imaging system; a second contact dispenser; a second stage that moves the second contact dispenser relative to the first bay and the second work area; and Mova A system comprising: An apparatus comprising:

77. 1. A modular system for preparing a library of samples for sequencing, comprising: a first assay bay, a first contact dispenser; a first work area, Work plate receptacle, Thermocyclers, and magnet a first work area comprising: a first drawer comprising a consumable area adapted to receive a sample plate adapted to contain samples and a plurality of consumables for interacting with the samples; a first assay bay comprising: a common bay comprising an analyzer area including an imaging system; and a mover operably coupled to the first assay bay and the common bay; Equipped with the first contact dispenser is linearly movable in a first direction between the consumable area and the first work area, and is configured to (i) move a sample plate in the consumable area to the work plate in the first work area, and (ii) move the plurality of consumables between the consumable area and the sample plate in the first work area; A modular system, wherein the mover is movable between the first assay bay and the common bay in the first direction and a second direction perpendicular to the first direction, and is configured to move the sample plate from the first work area to the analyzer area for analysis by the imaging system.

78. A modular bay for preparing a library of samples for sequencing, comprising: a contact dispenser; A work area, Work plate receptacle, Thermocyclers, and magnet, a work area comprising: a drawer comprising a consumable area adapted to receive a sample plate adapted to contain samples and a plurality of consumables for interacting with the samples; Equipped with The contact dispenser is movable linearly longitudinally between the consumable area and the work area and is configured to (i) move the sample plate in the consumable area to the work plate in the work area, and (ii) move the plurality of consumables.

79. 1. An apparatus comprising:

1. A pipette assembly comprising: a body including a base defining a plurality of pipette openings; a guide including a plurality of protrusions defining a pipette opening that aligns with the pipette opening of the base; a bar having a plurality of openings through which the projections of the guide extend; a plurality of pipettes coupled to the body and extending through the body and the pipette openings of the guide, each pipette having an end with a flange; a plurality of gaskets disposed between the protrusions and corresponding flanges of the pipette; a pipette cam assembly for moving the body away from the guide, moving the flange of the pipette toward the protrusion to compress the gasket, moving the body toward the guide, and moving the flange of the pipette away from the protrusion to relax the gasket; 12. An apparatus comprising: a pipette assembly comprising:

80. 80. The apparatus of claim 79, wherein compression of the gasket when the end of the pipette is placed within the pipette tip enables the gasket to form a bond with the pipette tip.

81. 81. The apparatus of any one of claims 79 to 80, wherein the gasket is relaxed when the end of the pipette is placed within a pipette tip, allowing the pipette tip to be uncoupled from the pipette.

82. 82. Apparatus according to any one of claims 79 to 81, wherein the guide comprises an outward channel, and the bar comprises first and second arms that extend into the outward channel of the guide.

83. The bar includes a first arm and a second arm, and the pipette cam assembly includes: a guide bearing coupled to the guide; a bar bearing coupled to the corresponding first arm and second arm; a camshaft including an inner lobe engaging the guide bearing and an outer lobe engaging the bar bearing; 82. The apparatus of any one of claims 79 to 81, comprising:

84. 84. The device of claim 83, wherein engagement of the inner lobe of the camshaft with the guide bearing moves the body away from the guide and moves the flange of the pipette toward the protrusion to compress the gasket.

85. 85. The apparatus of any one of claims 83 to 84, wherein the inner lobe of the camshaft engaging the guide bearing in a second position allows the guide to move towards the bar and move the flange of the pipette away from the protrusion to relax the gasket.

86. 86. The apparatus of claim 83, wherein engagement of the outer lobe of the camshaft with the rod bearing causes the bar to move toward the flange of the pipette, engaging a pipette tip carried by the pipette and biasing the pipette tip so that the pipette tip is released from the pipette assembly.

87. 87. Apparatus according to any one of claims 83 to 86, wherein one of the bar bearings faces one of the guide bearings.

88. 88. The apparatus of any one of claims 83 to 87, further comprising a torsion bar spring disposed between the bar and the guide to bias the bar bearing towards the corresponding outer lobe.

89. 89. Apparatus according to any one of claims 79 to 88, further comprising a guide spring disposed between the body and the guide to bias the body away from the guide.

90. 90. The apparatus of any one of claims 83 to 89, wherein the body comprises a first side and a second side, the camshaft comprises a first camshaft portion and a second camshaft portion, the first camshaft portion coupled to the first side of the body and the second camshaft portion coupled to the second side of the body.

91. 91. The apparatus of claim 90, wherein the first camshaft portion is spaced from the second camshaft portion.

92. 92. An apparatus as claimed in any one of claims 83 to 91, further comprising a motor and a gear set, said gear set coupled to said camshaft.

93. 93. The apparatus of claim 92, wherein movement of the motor rotates the camshaft.

94. 94. Apparatus according to any one of claims 92 to 93, wherein the gear set comprises first and second gears, first and second pinions, and a shaft connecting the first and second pinions.

95. 95. The apparatus of claim 94, wherein the body comprises a first side and a second side, the first gear is coupled to the first side of the body and the inner and outer lobes on the first side of the body, and the second gear is coupled to the second side of the body and the inner and outer lobes on the second side of the body.

96. 96. The apparatus of claim 95, wherein the first side and the second side of the body define a shaft opening, the shaft being rotatably coupled within the shaft opening.

97. 97. The apparatus of claim 96, wherein the shaft is spaced from the pipette.

98. 98. The apparatus of any one of claims 79 to 97, wherein the body comprises a first side and a second side and a wall defining a receptacle, the pipette being disposed within the receptacle.

99. 99. An apparatus according to any one of claims 79 to 98, wherein the pipettes each comprise a barrel, the apparatus further comprising a plurality of pistons disposed within and movable within corresponding barrels.

100. 100. The apparatus of claim 99, further comprising an actuator coupled to the piston for moving the piston between a retracted position and an extended position within the barrel.

101. 101. The apparatus of claim 100, wherein the actuator includes a ball screw.

102. 102. The apparatus of claim 101, wherein the actuator comprises a pair of linear rails and a lift, the lift coupled to the piston and the linear rails and movable by the ball screw.

103. 103. The apparatus of claim 102, wherein the lift is C-shaped and has ends, the apparatus further comprising a carriage coupled to a corresponding end of the lift and coupled to the linear rail.

104. 1. An apparatus comprising:

1. A thermocycler comprising: a base with a stop wall; a plate receptacle on the base; a cover assembly movably coupled to the base, a sled having a front wall, a rear wall, and a receptacle defined between said front wall and said rear wall; a cover disposed within the receptacle of the sled; a cover follower disposed within the receptacle of the sled and movably coupled to the cover; a cam assembly that moves the cover toward the base to cover the plate receptacle and moves the cover follower toward the base; a cover assembly comprising: a thermocycler comprising: The plate receptacle receives a plate having wells, and the thermocycler regulates the temperature of samples in the wells of the plate.

105. The cam assembly inner cam plates coupled to the sleds, each defining an inner cam slot; outer cam plates coupled to the base, each defining an outer cam slot; a cover bearing coupled to the cover and positioned to engage the stop wall; an inner slot bearing coupled to the cover and movably disposed within the inner cam slot; a cover follower bearing coupled to the cover follower and positioned to engage the rear wall of the sled; an outer slot bearing coupled to the cover follower and movably disposed within the outer cam slot; 105. The apparatus of claim 104, comprising:

106. 106. The apparatus of claim 105, wherein the cover bearing engages the stop wall, causing the inner slot bearing to move within the inner cam slot and the cover bearing to move along the stop wall, moving the cover toward the base and covering the plate receptacle.

107. 107. The apparatus of any one of claims 105 to 106, wherein the cover follower bearing engages the rear wall, causing the outer slot bearing to move within the outer cam slot and the cover follower bearing to move along the rear wall, causing the cover follower to move towards the base.

108. An apparatus according to any one of claims 104 to 107, further comprising a spring biasing the cover away from the cover follower.

109. An apparatus according to any one of claims 104 to 108, further comprising a guide rod movably coupling the cover and the cover follower.

110. 110. The apparatus of claim 109, wherein the cover includes a blind hole, the cover follower includes a through hole, and the guide rod is disposed within the corresponding blind hole in the cover and the through hole in the cover follower.

111. An apparatus according to any one of claims 109 to 110, wherein the spring surrounds a corresponding guide rod.

112. An apparatus according to any one of claims 105 to 111, wherein the cover defines a cover bearing receptacle in which the cover bearing is disposed.

113. Apparatus according to any one of claims 105 to 112, wherein the cover follower defines a cover follower bearing receptacle in which the cover follower bearing is disposed.

114. 114. The apparatus of any one of claims 104 to 113, further comprising a linear rail coupled to the base, and a carriage coupled to the rear wall and coupled to the linear rail.

115. 115. Apparatus according to any one of claims 104 to 114, wherein the stop wall comprises extensions having an opening defined therebetween, the front wall being sized to pass between the extensions.

116. 116. The apparatus of claim 115, wherein the cover bearing engages the extension.

117. 117. An apparatus according to any one of claims 104 to 116, further comprising a magnet and an actuator, the actuator moving the magnet relative to the plate receptacle.

118. 1. An apparatus comprising: A drawer comprising a platform, the drawer comprising: a plate receptacle coupled to the platform; a miniature liquid reagent well plate receptacle coupled to the platform, With the base, a first end wall having an inwardly extending lip forming a first groove with the base; a second end wall coupled to the base and having an inwardly extending lip forming a second groove with the base, the second end wall including a key; a miniature liquid reagent well plate receptacle comprising: a large liquid reagent well plate receptacle coupled to the platform, With the base, a first end wall having an inwardly extending lip that forms a first groove with the base of the large liquid reagent well plate receptacle; a second end wall coupled to the base and having an inwardly extending lip forming a second groove with the base of the large liquid reagent well plate receptacle, the second end wall including a key; a large liquid reagent well plate receptacle comprising: a dry well plate receptacle disposed on the platform and defining a waste reservoir compartment; and a waste reservoir having a wide portion including an inlet and a narrow portion extending from the wide portion and disposed within the waste reservoir compartment; 12. An apparatus comprising: a drawer comprising:

119. 119. The apparatus of claim 118, further comprising a central well plate support wall extending from the base and positioned between the first and second end walls of the miniature liquid reagent well plate receptacle.

120. 120. The apparatus of any one of claims 118 to 119, further comprising a central well plate support wall extending from the base and positioned between the first and second end walls of the large liquid reagent well plate receptacle.

121. 121. The apparatus of any one of claims 118 to 120, wherein the small liquid reagent well plate receptacle is located between the plate receptacle and the large liquid reagent well plate receptacle.

122. 122. The apparatus of any one of claims 118 to 121, wherein the large liquid reagent well plate receptacle is positioned between the small liquid reagent well plate receptacle and the dry well plate receptacle.

123. 123. An apparatus according to any one of claims 118 to 122, wherein the dry well plate receptacle is located between the large liquid reagent well plate receptacle and the wider portion of the waste reservoir that includes the inlet.

124. 124. An apparatus according to any one of claims 118 to 123, wherein the inlet comprises a rectangular inlet for receiving waste associated with a multi-tip pipette.

125. The apparatus of any one of claims 118 to 124, wherein the drawer further includes a tip receptacle.

126. 126. The apparatus of claim 125, wherein the tip receptacle is disposed between the large liquid reagent well plate receptacle and the dry well plate receptacle.

127. 1. An apparatus comprising:

1. A reagent well plate comprising: a first end wall having a male snap-fit ​​component; a second end wall having a male snap-fit ​​component; a panel coupled to and extending between the first end wall and the second end wall, the panel defining a plurality of reagent well receptacles and including a top surface; and a plurality of reagent wells having ends with annular collars, the reagent wells being positioned within the reagent well receptacle, the annular collars engaging the top surface; An apparatus comprising:

128. 128. The apparatus of claim 127, wherein the first end wall comprises a keying notch.

129. 129. The device of any one of claims 127 to 128, further comprising an impermeable barrier coupled to the end of the reagent well.

130. 130. The apparatus of any one of claims 127 to 129, further comprising a machine-readable code coupled to the panel.

131. 131. An apparatus according to any one of claims 127 to 130, wherein the reagent well plate comprises a miniature liquid reagent well plate.

132. 132. The apparatus of any one of claims 127 to 131, wherein the first end wall and the second end wall extend outwardly from the panel.

133. An apparatus according to any one of claims 127 to 132, wherein the panel is concave.

134. 134. The apparatus of claim 133, wherein the panel is substantially flat when the first end wall and the second end wall are coupled to a reagent well plate receptacle.

135. 135. An apparatus according to any one of claims 127 to 134, wherein each of the reagent wells comprises a second annular collar spaced longitudinally from the annular collar, and the panel is positioned between the annular collar of the corresponding reagent well and the second annular collar.

136. 136. The device of any one of claims 127 to 135, wherein the panel comprises a plurality of second reagent well receptacles having a different size than the reagent well receptacle, the second reagent well receptacles being positioned between the second end wall and the reagent well receptacle.

137. 137. The apparatus of claim 136, further comprising a bulk reagent well disposed within the second reagent well receptacle.

138. 138. The device of claim 137, further comprising an L-tab coupled to each of the bulk reagent wells.

139. 139. The device of claim 138, wherein the L-tab comprises a first leg coupled to the bulk reagent well and a second leg extending from the first leg at an angle corresponding to the angle of the second end wall.

140. 140. The apparatus of any one of claims 138 to 139, wherein the L-tabs are positioned within the dimensional envelope of the reagent well plate.

141. 141. Apparatus according to any one of claims 127 to 140, wherein the second end wall comprises a first wall section and a second wall section joined to form a recess.

142. 142. The apparatus of claim 141, wherein the L-tab is positioned within a dimensional envelope of the recess.

143. 143. The device of any one of claims 127 to 142, wherein the first end wall comprises a pair of first end wall portions and a pair of the male snap-fit ​​components, each first end wall portion including one of the male snap-fit ​​components.

144. 144. The device of any one of claims 127 to 143, wherein the second end wall comprises a pair of second end wall portions and a pair of the male snap-fit ​​components, each second end wall portion including one of the male snap-fit ​​components.

145. 145. The device of any one of claims 127-128 and 130-144, further comprising a plurality of impermeable barriers, each reagent well being covered by one of the impermeable barriers.

146. 146. An apparatus according to any one of claims 127 to 145, wherein each of the reagent wells comprises a second annular collar spaced longitudinally from the annular collar, and wherein a snap-fit ​​connection is formed between the plate, the annular collar, and the second annular collar.

147. 147. The device of any one of claims 127 to 146, wherein the male snap-fit ​​component includes a tapered tab.

148. 1. An apparatus comprising: A well plate, a rectangular wall including end walls and side walls, each of the end walls including a notch and a recess forming a handle extending between the side walls; a panel coupled to the rectangular wall, the panel defining a plurality of reagent well receptacles and including a top surface, the end walls and the side walls extending outwardly from the panel; a well plate comprising: a plurality of reagent wells having ends with annular collars, the reagent wells being positioned within the reagent well receptacle, the annular collars engaging the top surface; An apparatus comprising:

149. 149. The apparatus of claim 148, wherein the notches and recesses in adjacent plates form openings.

150. 150. A device as claimed in any one of claims 148 to 149, wherein the end wall comprising the handle forms a dog-bone shape.

151. An apparatus as claimed in any one of claims 148 to 150, wherein the rectangular wall and the panel form a step.

152. 152. The apparatus of claim 151, wherein the rectangular wall has ends that form openings sized to receive the steps of adjacent well plates.

153. 153. An apparatus according to any one of claims 148 to 152, wherein the panel comprises a plurality of rows of the reagent well receptacles.

154. A method according to any one of claims 148 to 153, wherein the panel comprises a row of the reagent well receptacles.

155. 155. An apparatus as described in any one of claims 148 to 154, further comprising a lid having a lid rectangular wall and a lid panel, the lid rectangular wall including lid end walls and lid side walls, each of the lid end walls including a lid notch forming a lid handle extending between the lid side walls.

156. 156. The device of claim 155, wherein the lid cutout and adjacent plate form an opening.

157. An apparatus according to any one of claims 155 to 156, wherein the lid rectangular wall and the lid panel form a lid step.

158. 158. The apparatus of claim 157, wherein the lid rectangular wall has ends that form a lid opening sized to receive the lid step of an adjacent lid.

159. 159. The apparatus of claim 158, wherein the rectangular wall and the panel form a step, and the lid opening is sized to receive the step of an adjacent well plate.

160. 1. An apparatus comprising: a consumable area for carrying a plurality of well plates, each of said well plates having a rectangular wall including a cutout; a plurality of assay bays, each comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out amplification and cleanup processes associated with preparing a sample library for sequencing; a common bay comprising a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of said samples for sequencing; a cross-bay gantry comprising grippers movable between the consumable area, the assay bay, and the common bay, the grippers comprising arms including inwardly extending extensions movable toward and away from each other; Equipped with The device, wherein the extension of the gripper is positionable within the notch of a corresponding well plate to move the well plate between any of the consumable bay, the assay bay plate receptacle, and the common bay plate receptacle.

161. 1. An apparatus comprising:

1. A library preparation system comprising: a consumable area carrying a plurality of well plates; a plurality of assay bays, each comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out amplification and cleanup processes associated with preparing a sample library for sequencing; a common bay comprising a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of said samples for sequencing; a cross-bay gantry including a gripper movable between the consumable area, the assay bay, and the common bay; a sample sipper assembly comprising a plurality of sipper and an actuator for moving the sipper relative to a plate receptacle of a library preparation system, the sample sipper assembly being associated with transferring the library of samples to a sequencing system; A library preparation system comprising: An apparatus comprising:

162. 162. The apparatus of claim 161, further comprising a fluid line fluidly coupling the sipper of the sample sipper assembly and the sequencing instrument.

163. 163. An apparatus according to any one of claims 161 to 162, further comprising a loading area comprising the sample sipper assembly and the plate receptacle.

164. 164. The apparatus of claim 163, wherein the loading area comprises a stage for moving the plate receptacle relative to the sample sipper assembly.

165. 1. An apparatus comprising: a plurality of assay bays, each comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out amplification and cleanup processes associated with preparing a library of samples for sequencing, said pipette assembly comprising: a body including a base defining a plurality of pipette openings; a guide including a plurality of protrusions defining a pipette opening that aligns with the pipette opening of the base; a bar having a plurality of openings through which the projections of the guide extend; a plurality of pipettes coupled to the body and extending through the body and the pipette openings of the guide, each pipette having an end with a flange; a plurality of gaskets disposed between the protrusions and corresponding flanges of the pipette; a pipette cam assembly for moving the body away from the guide, moving the flange of the pipette toward the protrusion to compress the gasket, and for moving the body toward the guide, moving the flange of the pipette away from the protrusion to relax the gasket; a plurality of assay bays comprising: a common bay comprising a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of said samples for sequencing; and a cross-bay gantry including a gripper movable between the assay bay and the common bay; An apparatus comprising:

166. 166. The device of claim 165, wherein the gasket is compressed when the end of the pipette is placed within the pipette tip, allowing the gasket to form a bond with the pipette tip.

167. 167. An apparatus according to any one of claims 165 to 166, wherein the gasket is relaxed when the end of the pipette is placed within the pipette tip, allowing the pipette tip to be disengaged from the pipette.

168. 168. An apparatus according to any one of claims 165 to 167, wherein the guide comprises an outward channel, and the bar comprises a first arm and a second arm that extend into the outward channel of the guide.

169. The bar includes a first arm and a second arm, and the pipette cam assembly includes: a guide bearing coupled to the guide; a bar bearing coupled to the corresponding first arm and second arm; a camshaft including an inner lobe engaging the guide bearing and an outer lobe engaging the bar bearing; 169. Apparatus according to any one of claims 165 to 168, comprising:

170. 170. The device of claim 169, wherein engagement of the inner lobe of the camshaft with the guide bearing moves the body away from the guide and moves the flange of the pipette toward the protrusion to compress the gasket.

171. 171. An apparatus according to any one of claims 169 to 170, wherein engagement of the inner lobe of the camshaft with the guide bearing in a second position allows the guide to move towards the bar and move the flange of the pipette away from the protrusion to relax the gasket.

172. 171. The apparatus of any one of claims 168 to 170, wherein engagement of the outer lobe of the camshaft with the rod bearing causes the bar to move toward the flange of the pipette, engaging a pipette tip carried by the pipette and biasing the pipette tip so that the pipette tip is released from the pipette assembly.

173. 173. Apparatus according to any one of claims 169 to 172, wherein one of the bar bearings faces one of the guide bearings.

174. 174. An apparatus as claimed in any one of claims 169 to 173, further comprising a torsion spring disposed between the bar and the guide to bias the bar bearing towards the corresponding outer lobe.

175. 175. An apparatus according to any one of claims 165 to 174, further comprising a guide spring disposed between the body and the guide to bias the body away from the guide.

176. 176. An apparatus as described in any one of claims 169 to 175, wherein the body has a first side and a second side, the camshaft has a first camshaft portion and a second camshaft portion, the first camshaft portion coupled to the first side of the body and the second camshaft portion coupled to the second side of the body.

177. 177. The apparatus of claim 176, wherein the first camshaft portion is spaced from the second camshaft portion.

178. An apparatus as described in any one of claims 169 to 177, further comprising a motor and a gear set, the gear set coupled to the camshaft.

179. 179. The apparatus of claim 178, wherein movement of the motor rotates the camshaft.

180. An apparatus as described in any one of claims 178 to 179, wherein the gear set comprises first and second gears, first and second pinions, and a shaft connecting the first and second pinions.

181. 181. The device of claim 180, wherein the body has a first side and a second side, the first gear is coupled to the first side of the body and the inner lobe and the outer lobe on the first side of the body, and the second gear is coupled to the second side of the body and the inner lobe and the outer lobe on the second side of the body.

182. 182. The device of any one of claims 180 to 181, wherein the first and second sides of the body define a shaft opening, and the shaft is rotatably coupled within the shaft opening.

183. 183. An apparatus according to any one of claims 180 to 182, wherein the shaft is spaced apart from the pipette.

184. 184. An apparatus according to any one of claims 165 to 183, wherein the body comprises a first side and a second side and a wall defining a receptacle, the pipette being disposed within the receptacle.

185. 185. An apparatus according to any one of claims 165 to 184, wherein the pipettes each comprise a barrel, and the apparatus further comprises a plurality of pistons disposed within and movable within corresponding barrels.

186. 186. The apparatus of claim 185, further comprising an actuator coupled to the piston for moving the piston between a retracted position and an extended position within the barrel.

187. 187. The apparatus of claim 186, wherein the actuator includes a ball screw.

188. 188. The apparatus of claim 187, wherein the actuator comprises a pair of linear rails and a lift, the lift being coupled to the piston and the linear rails and movable by the ball screw.

189. 189. The apparatus of claim 188, wherein the lift is C-shaped and has ends, the apparatus further comprising a carriage coupled to the corresponding ends of the lift and coupled to the linear rail.

190. 190. The apparatus of any one of claims 165 to 189, further comprising a sample sipper assembly comprising a plurality of sippers and an actuator for moving the sipper relative to the well plate, the sample sipper assembly being associated with transferring the library of samples to a sequencing system.

191. 1. An apparatus comprising: a plurality of assay bays, each comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out amplification and clean-up processes associated with preparing a library of samples for sequencing, said thermocycler comprising: a base having a stop wall; a plate receptacle on the base; a cover assembly movably coupled to the base, a sled having a front wall, a rear wall, and a receptacle defined between said front wall and said rear wall; a cover disposed within the receptacle of the sled; a cover follower disposed within the receptacle of the sled and movably coupled to the cover; a cam assembly that moves the cover toward the base to cover the plate receptacle and moves the cover follower toward the base; a cover assembly comprising: a thermocycler comprising: a plurality of assay bays, wherein the plate receptacle receives a plate having wells, and the thermocycler regulates the temperature of samples in the wells of the plate; a common bay comprising a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of said samples for sequencing; and a cross-bay gantry including a gripper movable between the assay bay and the common bay; An apparatus comprising:

192. The cam assembly inner cam plates coupled to the sleds, each defining an inner cam slot; outer cam plates coupled to the base, each defining an outer cam slot; a cover bearing coupled to the cover and positioned to engage the stop wall; an inner slot bearing coupled to the cover and movably disposed within the inner cam slot; a cover follower bearing coupled to the cover follower and positioned to engage the rear wall of the sled; an outer slot bearing coupled to the cover follower and movably disposed within the outer cam slot; 192. The apparatus of claim 191, comprising:

193. 193. The apparatus of claim 192, wherein the cover bearing engages the stop wall, causing the inner slot bearing to move within the inner cam slot and the cover bearing to move along the stop wall, moving the cover toward the base to cover the plate receptacle.

194. An apparatus as described in any one of claims 192 to 193, wherein the cover follower bearing engages the rear wall, causing the outer slot bearing to move within the outer cam slot and the cover follower bearing to move along the rear wall, causing the cover follower to move towards the base.

195. 195. An apparatus as claimed in any one of claims 191 to 194, further comprising a spring which biases the cover away from the cover follower.

196. 196. An apparatus according to any one of claims 191 to 195, further comprising a guide rod movably coupling the cover and the cover follower.

197. 197. The apparatus of claim 196, wherein the cover includes a blind hole, the cover follower includes a through hole, and the guide rod is positioned within the corresponding blind hole in the cover and the through hole in the cover follower.

198. 198. An apparatus according to any one of claims 196 to 197, wherein the spring surrounds a corresponding guide rod.

199. An apparatus as claimed in any one of claims 191 to 198, wherein the cover defines a cover bearing receptacle in which the cover bearing is disposed.

200. 200. An apparatus according to any one of claims 191 to 199, wherein the cover follower defines a cover follower bearing receptacle in which the cover follower bearing is disposed.

201. An apparatus as claimed in any one of claims 191 to 200, further comprising a linear rail coupled to the base, and a carriage coupled to the rear wall and coupled to the linear rail.

202. 202. An apparatus as claimed in any one of claims 191 to 201, wherein the stop wall comprises extensions having an opening defined therebetween, the front wall being sized to pass between the extensions.

203. 203. The apparatus of claim 202, wherein the cover bearing engages the extension.

204. An apparatus as described in any one of claims 191 to 203, further comprising an actuator, the actuator moving the magnet relative to the plate receptacle.

205. 1. An apparatus comprising: a plurality of assay bays, each comprising a drawer comprising a platform, an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out amplification and clean-up processes associated with preparing a library of samples for sequencing, said drawer comprising: a plate receptacle coupled to the platform; a miniature liquid reagent well plate receptacle coupled to the platform, With the base, a first end wall having an inwardly extending lip that forms a first groove with the base; a second end wall coupled to the base and having an inwardly extending lip forming a second groove and including a key; and a miniature liquid reagent well plate receptacle comprising: a large liquid reagent well plate receptacle coupled to the platform, With the base, a first end wall having an inwardly extending lip that forms a first groove with the base of the large liquid reagent well plate receptacle; a second end wall coupled to the base and having an inwardly extending lip forming a second groove with the base of the large liquid reagent well plate receptacle, the second end wall including a key; a large liquid reagent well plate receptacle comprising: a dry well plate receptacle disposed on the platform and defining a waste reservoir compartment; and a waste reservoir having a wide portion including an inlet and a narrow portion extending from the wide portion and disposed within the waste reservoir compartment; Drawer with a plurality of assay bays comprising: a common bay comprising a common bay plate receptacle and an imaging system for performing a quantification process associated with preparing a library of said samples for sequencing; and a cross-bay gantry including a gripper movable between the assay bay and the common bay; An apparatus comprising:

206. 206. The apparatus of claim 205, further comprising a central well plate support wall extending from the base and positioned between the first end wall and the second end wall of the miniature liquid reagent well plate receptacle.

207. 207. The apparatus of any one of claims 205-206, further comprising a central well plate support wall extending from the base and positioned between the first and second end walls of the large liquid reagent well plate receptacle.

208. 208. An apparatus according to any one of claims 205 to 207, wherein the small liquid reagent well plate receptacle is located between the plate receptacle and the large liquid reagent well plate receptacle.

209. 209. The apparatus of any one of claims 205 to 208, wherein the large liquid reagent well plate receptacle is located between the small liquid reagent well plate receptacle and the dry well plate receptacle.

210. 210. An apparatus according to any one of claims 205 to 209, wherein the dry well plate receptacle is located between the large liquid reagent well plate receptacle and the wider portion of the waste reservoir that includes the inlet.

211. 211. An apparatus according to any one of claims 205 to 210, wherein the inlet comprises a rectangular inlet for receiving waste associated with a multi-tip pipette.

212. The apparatus of any one of claims 205 to 211, wherein the drawer further includes a tip receptacle.

213. 213. The apparatus of claim 212, wherein the tip receptacle is positioned between the large liquid reagent well plate receptacle and the dry well plate receptacle.

214. 1. A library preparation system for preparing a library of samples for sequencing, comprising: a work area for preparing a library of samples for genome sequencing; a communication interface, and one or more processors communicatively coupled to the communication interface and configured to communicate with the sequencer via the communication interface by sending or receiving information related to the library of samples; A library preparation system comprising:

215. To communicate with the sequencer, the one or more processors:

215. The library preparation system of claim 214, configured to transmit identification information for the library of samples to the sequencer via the communications interface.

216. To communicate with the sequencer, the one or more processors:

216. The library preparation system of any one of claims 214 to 215, configured to send one or more run parameters for sequencing the library of samples to the sequencer via the communications interface.

217. To communicate with the sequencer, the one or more processors:

217. The library preparation system of any one of claims 214 to 216, configured to send an indication of the preparation status of the library of samples to the sequencer via the communications interface.

218. To communicate with the sequencer, the one or more processors:

218. The library preparation system of any one of claims 214 to 217, configured to send instructions to the sequencer via a communications interface indicating a particular lane of a flow cell for the sequencer to sequence a particular sample of the library of samples.

219. To communicate with the sequencer, the one or more processors 219. The library preparation system of any one of claims 214 to 218, configured to receive status information from the sequencer via the communications interface.

220. To communicate with the sequencer, the one or more processors 220. The library preparation system of any one of claims 214 to 219, configured to receive an indication from the sequencer via the communications interface that the sequencer is ready to receive the library of samples.

221. and a fluid line configured to couple to the library preparation system and the sequencer.

221. The library preparation system of claim 220, wherein the library preparation system sends the library of samples to the sequencer via the fluid line in response to receiving the indication that the sequencer is ready to receive the library of samples.

222. The work area includes: a work plate, and Thermocycler 222. The library preparation system of any one of claims 214 to 221, comprising:

223. Contact dispensers, and a drawer comprising a consumable area adapted to receive a sample plate adapted to contain samples and a plurality of consumables for interacting with the samples; 223. The library preparation system of any one of claims 214 to 222, wherein the contact dispenser is configured to (i) move the sample plate in the consumable area to the work plate in the work area, and (ii) move the plurality of consumables.

224. 224. The library preparation system of any one of claims 214 to 223, wherein the communication interface comprises a wired communication link attached to the library preparation system and the sequencer.

225. 1. A method for communicating between a library preparation system and a sequencer, comprising: preparing a library of samples for genome sequencing with a library preparation system having a contact dispenser and a work area for interacting one or more consumables with the samples; communicating with the sequencer by sending or receiving information related to the library of samples via a communications interface, by one or more processors within the library preparation system; A method comprising:

226. Communicating with the sequencer includes:

226. The method of claim 225, comprising transmitting, by the one or more processors, identification information for the library of samples to the sequencer via the communications interface.

227. Communicating with the sequencer includes:

227. The method of any one of claims 225-226, comprising sending, by the one or more processors, via the communications interface to the sequencer, one or more run parameters for sequencing the library of samples.

228. Communicating with the sequencer includes:

228. The method of any one of claims 225 to 227, comprising sending, by the one or more processors, an indication of the preparation status of the library of samples to the sequencer via the communications interface.

229. Communicating with the sequencer includes:

229. The method of any one of claims 225 to 228, comprising sending, by the one or more processors, instructions to the sequencer via the communications interface indicating a particular lane of a flow cell for the sequencer to sequence a particular sample of the library of samples.

230. Communicating with the sequencer includes: A method according to any one of claims 225 to 229, comprising receiving, at the one or more processors, status information from the sequencer via the communications interface.

231. Communicating with the sequencer includes:

231. The library preparation system of any one of claims 225 to 230, wherein the one or more processors are configured to receive an indication from the sequencer via the communications interface that the sequencer is ready to receive the library of samples.

232. 232. The library preparation system of any one of claims 225 to 231, further comprising, in response to receiving the indication that the sequencer is ready to receive the library of samples, sending the library of samples by the library preparation system to the sequencer via fluid lines coupled to the library preparation system and the sequencer.

233. 233. The method of any one of claims 225 to 232, wherein the communication interface comprises a wired communication link attached to the library preparation system and the sequencer.

234. 1. A method comprising: receiving a miniature liquid reagent well plate with a miniature liquid reagent well plate receptacle on a platform of a drawer, wherein a snap-fit ​​connection is formed when the miniature liquid reagent well plate receptacle receives the miniature liquid reagent well plate; receiving a large liquid reagent well plate with a large liquid reagent well plate receptacle coupled to the platform of the drawer, wherein a snap-fit ​​connection is formed when the large liquid reagent well plate receptacle receives the large liquid reagent well plate; receiving a dry reagent well plate by a dry well plate receptacle disposed on the platform and defining a waste reservoir compartment, the waste reservoir being disposed within the waste reservoir compartment; receiving the drawer into one of a plurality of assay bays of a library preparation system, the library preparation system including the assay bays and a common bay, the assay bays performing amplification and cleanup processes, respectively, associated with preparing a library of samples for sequencing, and the common bay performing library quantification, library pooling, denaturation, and dilution processes associated with preparing the library of samples for sequencing; A method comprising:

235. The method of claim 234, wherein each assay bay includes an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet for carrying out the amplification and cleanup processes associated with preparing a library of samples for sequencing.

236. 236. The method of any one of claims 234-235, wherein the small liquid reagent well plate comprises a first end wall having a male snap-fit ​​component, a second end wall having a male snap-fit ​​component, a panel coupled to and extending between the first and second end walls, and a plurality of reagent wells disposed within the reagent well receptacle.

237. 237. The method of any one of claims 234 to 236, wherein the miniature liquid reagent well plate receptacle comprises a base, a first end wall having an inwardly extending lip that forms a first groove with the base, and a second end wall coupled to the base and having an inwardly extending lip that forms a second groove with the base, the second end wall comprising a key.

238. The method of any one of claims 234 to 237, wherein receiving the small liquid reagent well plate by the small liquid reagent well plate receptacle on the platform of the drawer comprises a keying notch in the small liquid reagent well plate receiving a key in the small liquid reagent well plate receptacle.

239. 239. The method of any one of claims 234 to 238, wherein the large liquid reagent well plate comprises a first end wall coupled to the base with a male snap-fit ​​component, a second end wall with a male snap-fit ​​component, a panel coupled to and extending between the first and second end walls, and a plurality of reagent wells disposed within the reagent well receptacle.

240. 240. The method of any one of claims 234-239, wherein the large liquid reagent well plate receptacle comprises a base, a first end wall coupled to the base and having an inwardly extending lip that forms a first groove with the base, and a second end wall coupled to the base and having an inwardly extending lip that forms a second groove with the base, the second end wall comprising a key.

241. The method of any one of claims 234 to 240, wherein receiving the large liquid reagent well plate by the large liquid reagent well plate receptacle on the platform of the drawer comprises a keying notch in the large liquid reagent well plate receiving a key in the large liquid reagent well plate receptacle.

242. The method of any one of claims 234 to 241, wherein receiving the small liquid reagent well plate by the small liquid reagent well plate receptacle on the platform of the drawer includes supporting the panel of the small liquid reagent well plate using a central well plate support wall extending from the base of the small liquid reagent well plate receptacle and positioned between a first end wall and a second end wall of the small liquid reagent well plate receptacle.

243. 243. The method of claim 242, wherein supporting the panel of the small liquid reagent well plate comprises supporting the panel using a plurality of central well plate support walls of the small liquid reagent well plate receptacle.

244. A method according to any one of claims 242 to 243, wherein the panel of the small liquid reagent well plate is supported by the central well plate of the small liquid reagent well plate receptacle, allowing the panel of the small liquid reagent well plate to be substantially flat.

245. 245. The method of any one of claims 234 to 244, wherein the coupling between the small liquid reagent well plate and the small liquid reagent well plate receptacle allows the panel of the small liquid reagent well plate to be substantially flat.

246. The method of any one of claims 234 to 245, wherein receiving the large liquid reagent well plate by the large liquid reagent well plate receptacle on the platform of the drawer includes supporting the panel of the large liquid reagent well plate using a central well plate support wall extending from the base of the small liquid reagent well plate receptacle and positioned between a first end wall and a second end wall of the small liquid reagent well plate receptacle.

247. 247. The method of claim 246, wherein supporting the panel of the large liquid reagent well plate comprises supporting the panel using a plurality of central well plate support walls of the large liquid reagent well plate receptacle.

248. 248. The method of any one of claims 245 to 247, wherein the panel of the large liquid reagent well plate is supported by the central well plate support of the large liquid reagent well plate receptacle, allowing the panel of the large liquid reagent well plate to be substantially flat.

249. 249. The method of any one of claims 234 to 248, wherein the coupling between the large liquid reagent well plate and the large liquid reagent well plate receptacle allows the panel of the large liquid reagent well plate to be substantially flat.

250. 250. The method of any one of claims 234 to 249, wherein the large liquid reagent well plate comprises a reagent well receptacle and a second reagent well receptacle, the second reagent well receptacle having a different size than the reagent well receptacle, and a bulk reagent well is disposed within the second reagent well receptacle.

251. 1. A method comprising: performing amplification and cleanup processes on samples contained in well plates placed on plate receptacles of a thermocycler on an assay bay of a library preparation system; using a gripper to remove the well plate from the plate receptacle of the thermocycler by placing the gripper in a notch in the well plate and moving the gripper away from the plate receptacle; using the gripper to move the well plate to a common bay of the library preparation system; performing a library quantification process in said common bay; A method comprising:

252. 252. The method of claim 251, further comprising performing a library pooling process in the common bay.

253. 253. A method according to any one of claims 251 to 252, further comprising carrying out at least one of a denaturation process or a dilution process associated with the common bay.

254. The well plate is a rectangular wall including end walls and side walls, each of the end walls including a notch and a recess forming a handle extending between the side walls; a panel coupled to and extending between the rectangular walls, the panel defining a plurality of reagent well receptacles and including a top surface, the end wall, and the side wall extending outwardly from the panel; a plurality of reagent wells having ends with annular collars, the reagent wells being disposed within the reagent well receptacle, the annular collars engaging the top surface; 254. The method of any one of claims 251 to 253, comprising:

255. 255. The method of any one of claims 251 to 254, further comprising using the gripper to remove a lid from the well plate in the plate receptacle.

256. 256. The method of claim 255, wherein removing the lid comprises positioning the gripper within a lid notch that forms a lid handle extending between lid sidewalls of the lid, and moving the lid away from the well plate.

257. 257. The method of any one of claims 251 to 256, further comprising using the gripper to move the well plate from the consumable area to the assay bay.

258. 258. The method of claim 257, wherein moving the well plate comprises positioning the gripper within a notch in the well plate that forms a handle for the well plate, and moving the well plate away from the consumable area.

259. 259. The method of any one of claims 257-258, wherein removing the well plate from the consumable area comprises removing the well plate from a stack of well plates in the consumable area.

260. 1. A method comprising: inserting an end of a pipette of a pipette assembly of an assay bay of a library preparation system and a gasket carried by said pipette into a pipette tip on a drawer of said assay bay; compressing the gasket of the pipette assembly to couple the pipette tip and the pipette assembly; dispensing reagents into well plates on plate receptacles of the assay bay using the pipette assembly and the pipette tips; performing an amplification process and a cleanup process on the samples contained in the well plates in the plate receptacle; A method comprising:

261. 261. The method of claim 260, wherein compressing the gasket comprises moving a body of the pipette assembly away from a guide of the pipette assembly and moving a flange of the pipette towards a protrusion of the guide to compress the gasket.

262. 262. The method of claim 261, wherein moving the body of the pipette assembly away from the guide of the pipette assembly and moving the flange of the pipette towards a protrusion of the guide to compress the gasket includes using a pipette cam assembly.

263. A method according to any one of claims 260 to 262, wherein the gasket is compressed by moving the body of the pipette assembly away from the guide of the pipette assembly and moving a flange of the pipette towards a protrusion of the guide, thereby engaging an inner lobe of a camshaft of a pipette cam assembly of the pipette assembly with a guide bearing of the pipette assembly.

264. 264. The method of any one of claims 260 to 263, further comprising relaxing the gasket to allow the pipette tip to be separated from the pipette assembly.

265. 265. The method of claim 264, wherein loosening the gasket comprises moving a body of the pipette assembly toward a guide of the pipette assembly and moving a flange of the pipette away from a protrusion of the guide to loosen the gasket.

266. 266. The method of claim 265, wherein moving the guide of the pipette assembly toward the bar of the pipette assembly and moving the flange of the pipette away from the protrusion of the guide to loosen the gasket includes using a pipette cam assembly.

267. The method of any one of claims 260 to 266, further comprising positioning an inner lobe of a camshaft of a pipette cam assembly of the pipette assembly in a second position relative to a guide bearing of the pipette assembly, thereby allowing a flange of the pipette to move away from a protrusion of the guide of the pipette assembly and relaxing the gasket, thereby allowing the body to move toward the guide of the pipette assembly, and allowing the flange of the pipette to move away from the protrusion of the guide and relaxing the gasket.

268. 268. The method of claim 267, further comprising releasing the pipette tip from the pipette assembly.

269. 269. The method of claim 268, wherein releasing the pipette tip from the pipette assembly comprises moving the bar toward the flange, engaging the pipette tip with the bar, and releasing the pipette tip from the pipette assembly.

270. 268. The method of any one of claims 258 to 267, further comprising using an actuator to move a piston within the barrel of the pipette between a retracted position and an extended position.

271. 1. A method comprising: moving a sled of a cover assembly of a thermocycler toward a stop wall of the base of the thermocycler, a cover disposed in a receptacle of the sled, and a cover follower disposed in the receptacle of the sled and movably coupled to the cover; engaging the stop wall with a cover bearing coupled to the cover; engaging a rear wall of the sled with a cover follower bearing coupled to the cover follower; moving an inner slot bearing within an inner cam slot of an inner cam plate to move the cover toward a plate receptacle, the inner slot bearing coupled to the cover and the inner cam plate coupled to the sled; moving an outer slot bearing within an outer cam slot of an outer cam plate to move the cover follower toward the base, the outer slot bearing being coupled to the cover follower and the outer cam plate being coupled to the plate; A method comprising:

272. 272. The method of claim 271, further comprising performing an amplification process on the sample in the well plate placed on the plate receptacle.

273. 273. The method of any one of claims 271 to 272, further comprising performing a cleanup process on the sample in the well plate disposed on the plate receptacle.

274. 274. The method of claim 273, wherein performing a cleanup process includes moving a magnet toward the well plate on the plate receptacle.

275. A method according to any one of claims 271 to 274, wherein the cover bearing engaging the stop wall moves the inner slot bearing within the inner cam slot, moving the cover bearing along the stop wall and moving the cover towards the base to cover the plate receptacle.

276. A method according to any one of claims 271 to 275, wherein the cover follower bearing engaging the rear wall causes the outer slot bearing to move within the outer cam slot, causing the cover follower bearing to move along the rear wall and move the cover follower towards the base.

277. 277. The method of any one of claims 271 to 276, further comprising biasing the cover away from the cover follower.

278. 1. A method comprising: performing amplification and clean-up processes on samples in a well plate in a plurality of assay bays, each assay bay comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet; moving the sample from the assay bay to a common bay using a cross-bay gantry; performing a library quantification process on the samples in the common bay; archiving said library of samples; A method comprising:

279. 279. The method of claim 278, wherein archiving the library of samples comprises sealing the samples.

280. 280. The method of any one of claims 278 to 279, wherein archiving the library of samples comprises freezing the samples.

281. 1. A method comprising: performing amplification and clean-up processes on samples in a well plate in a plurality of assay bays, each assay bay comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet; moving the sample from the assay bay to a common bay using a cross-bay gantry; performing a library quantification process and a library pooling process on the samples in the common bay; A method comprising:

282. 282. The method of claim 281, wherein the library pooling process comprises preparing an equimolar pool using the sample based on the quantification value determined by the library quantification process.

283. 283. The method of any one of claims 281 to 282, further comprising archiving the remaining portion of the library of samples.

284. 284. The method of claim 283, wherein archiving the library of samples comprises sealing the samples.

285. 285. The method of any one of claims 283 to 284, wherein archiving the library of samples comprises freezing the samples.

286. 1. A method comprising: performing amplification and clean-up processes on samples in a well plate in a plurality of assay bays, each assay bay comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet; moving the sample from the assay bay to a common bay using a cross-bay gantry; preparing a sequencing-ready pool of samples in said common bay; A method comprising:

287. 287. The method of claim 286, wherein preparing a sequencing-ready pool of the samples in the common bay comprises performing a library quantification process and a library pooling process on the samples.

288. 288. The method of any one of claims 286 to 287, wherein preparing a sequencing-ready pool of the samples in the common bay comprises performing a denaturing process on the samples.

289. 289. The method of any one of claims 286 to 288, wherein preparing a sequencing-ready pool of the samples in the common bay comprises performing a dilution process on the samples.

290. 1. A method comprising: performing amplification and clean-up processes on samples in a well plate in a plurality of assay bays, each assay bay comprising an assay bay plate receptacle, a pipette assembly, a thermocycler, and a magnet; moving the sample from the assay bay to the common bay using a cross-bay gantry; preparing a sequencing-ready pool of samples in said common bay; transferring the sequencing-ready pool of the library of samples to a sequencer; A method comprising:

291. 291. The method of claim 290, wherein transferring the sequencing-ready pool of samples to the sequencer comprises transferring the sample library to a sequencing system using a sample shipper assembly.

292. 292. The method of any one of claims 290 to 291, wherein preparing a sequencing-ready pool of samples in the common bay comprises performing a library quantification process and a library pooling process on the samples.

293. 293. The method of any one of claims 290 to 292, wherein preparing a sequencing-ready pool of the samples in the common bay comprises performing a denaturation process on the samples.

294. 294. The method of any one of claims 290 to 293, wherein preparing a sequencing-ready pool of samples in the common bay comprises performing a dilution process on the samples.

295. 1. An apparatus comprising:

1. A library preparation system comprising: an assay bay for carrying out amplification and clean-up processes; and a common bay for carrying out the quantification process, A library preparation system comprising: An apparatus comprising:

296. 1. An apparatus comprising:

1. A library preparation system comprising: a sample sipper assembly including a sipper coupled to the sample cartridge; a library preparation system comprising:

1. A sequencing instrument comprising: a flow cell interface coupled to a flow cell having a plurality of channels; a central valve and an auxiliary waste fluid line coupled to the central valve and coupled to a waste reservoir, the central valve being coupled to the flow cell interface and movable between a first position fluidly connecting the inlets of the plurality of channels to the auxiliary waste fluid line and a second position fluidly connecting a reagent reservoir and the plurality of channels; and a sample loading assembly disposed between the flow cell interface and the sample sipper assembly of the library preparation system, a body carrying a plurality of sample valves and defining a plurality of sample ports and a plurality of flow cell ports, each sample port being coupled via a sample fluid line to a corresponding sipper of said sample sipper assembly; a sample loading assembly comprising: A sequencing instrument comprising: Equipped with An apparatus wherein the sample sipper assembly of the library preparation system is positioned downstream of the flow cell interface of the sequencing instrument.

297. 297. The device of claim 296, wherein each flow cell port is coupled to a corresponding port of the flow cell interface and associated with one of the plurality of channels of the flow cell via a flow cell fluid line.

298. 298. The apparatus of any one of claims 296 to 297, wherein the sample valve is movable to fluidly couple a sipper of the library preparation system, a sample port of the sequencing instrument, and a corresponding outlet of one of the plurality of channels of the flow cell.

299. 300. The apparatus of any one of claims 296 to 298, wherein the sample valve is movable to fluidly disconnect a sipper of the library preparation system, a sample port of the sequencing instrument, and a corresponding outlet of one of the plurality of channels of the flow cell.

300. 300. An apparatus according to any one of claims 296 to 299, wherein the sample valve is operable to individually load each channel of the plurality of channels of the flow cell.

301. The apparatus of any one of claims 296 to 300, wherein the sequencing instrument further comprises a plurality of pumps, and the body of the sample loading assembly further defines a plurality of pump ports, each pump port being coupled to one of the pumps of the plurality of pumps via a pump channel fluid line.

302. The apparatus of claim 301, wherein each sample valve is operable to fluidly couple a sipper of the sample sipper assembly of the library preparation system to a corresponding pump of the plurality of pumps of the sequencing instrument, and to fluidly couple one of the plurality of pumps to a corresponding channel of the plurality of channels of the flow cell.

303. 303. An apparatus according to any one of claims 301 to 302, wherein the pump is operable to individually control fluid flow in each of the plurality of channels of the flow cell.

304. An apparatus according to any one of claims 296 to 303, wherein the outlets of the plurality of channels are fluidly connectable to a waste reservoir.

305. 305. The apparatus of claim 304, wherein the sequencing instrument comprises a pump manifold assembly comprising a plurality of pumps, the pump manifold assembly fluidly coupling the outlets of the plurality of channels to the waste reservoir.

306. The apparatus of any one of claims 301 to 305, wherein the sequencing device comprises a pump manifold assembly comprising the pump and a cache, and the sequencing device further comprises a bypass valve and a bypass fluid line connecting the bypass valve and the cache.

307. The apparatus of claim 306, wherein the sequencing instrument further comprises a shared line valve, a plurality of dedicated reagent fluid lines, and a shared reagent fluid line, the shared reagent fluid line connecting the shared line valve and the central valve and adapted to flow one or more reagents to the flow cell, and each dedicated reagent fluid line connecting the bypass fluid line and the central valve and adapted to flow one or more reagents toward the flow cell.

308. 308. The apparatus of any one of claims 306-307, wherein the pump manifold assembly carries a plurality of pump valves and cache valves and includes a plurality of pump channel fluid lines, a plurality of pump fluid lines, a shared fluid line, a cache fluid line, and a main waste fluid line, the cache fluid lines coupled to the cache and the cache valves and coupled between the cache and the cache valves, each pump valve coupled to a corresponding pump channel fluid line, a corresponding pump fluid line, and the shared fluid line, and the cache valve coupled to the cache fluid line, the main waste fluid line, and the shared fluid line.

309. The apparatus of claim 308, wherein the pump valve and the pump are operable to individually control fluid flow in each channel of the plurality of channels of the flow cell, and the pump valve, the cache valve, and the pump are operable to control fluid flow between the bypass fluid line and the shared fluid line.

310. 310. The apparatus of claim 309, wherein the pump valve, the cache valve, and the pump are operable to control fluid flow between the shared fluid line and the main waste fluid line.

311. 1. An apparatus comprising:

1. A library preparation system comprising: A sample sipper assembly including a sipper coupled to a sample cartridge a library preparation system comprising:

1. A sequencing instrument comprising: one or more valves adapted to be coupled to corresponding reagent reservoirs; a flow cell interface adapted to be coupled to the flow cell; and a pump adapted to load the sample of interest into a channel of the flow cell via the flow cell interface associated with an outlet of the flow cell and a corresponding sipper of the sample sipper assembly; a sequencing instrument comprising: An apparatus comprising:

312. The apparatus of claim 311, wherein the sequencing instrument further comprises a pump manifold assembly having a plurality of pumps including the pump and a plurality of pump valves, each pump and corresponding pump valve operable to individually control the flow of the target sample between each sipper of a sample sipper assembly of the library preparation system and a corresponding channel of the flow cell.

313. The apparatus of any one of claims 311 to 312, wherein the sequencing instrument further comprises a sample loading assembly having a plurality of sample valves, each sample valve operable to individually load the target sample into each channel of the plurality of channels of the flow cell.

314. The apparatus of any one of claims 311 to 313, further comprising a flow cell assembly including the flow cell having a plurality of channels and a flow cell manifold, the flow cell manifold including an inlet, a plurality of fluid lines, and a plurality of outlets, each outlet of the flow cell manifold being coupled to a corresponding channel of the flow cell.

315. 1. A method comprising: moving a first sample valve of the one or more sample valves to a first position to fluidly couple a first sipper of the sipper manifold assembly of the library preparation system with a first pump of the sequencing instrument; drawing a first sample of interest from the library preparation system through the first sipper of the sipper manifold assembly toward the first pump of the sequencing instrument; moving the first sample valve to a second position to fluidly couple the first pump with a channel of a flow cell coupled to a flow cell interface of the sequencing instrument; pumping the first target sample into the first channel of the flow cell through an outlet of the first channel; A method comprising:

316. moving a second sample valve of the one or more sample valves to a first position to fluidly couple a second sipper of the sipper manifold assembly of the library preparation system with a second pump of the sequencing instrument; drawing a second sample of interest from the library preparation system through the second shipper of the shipper manifold assembly toward the second pump of the sequencing instrument; moving the second sample valve to a second position to fluidly couple the second pump with a second channel of the flow cell coupled to the flow cell interface of the sequencing instrument; pumping the second target sample into the second channel of the flow cell through an outlet of the second channel; The method of claim 315, further comprising:

317. 317. The method of any one of claims 315-316, further comprising fluidly coupling a reagent reservoir to the inlet of the channel of the flow cell.

318. 318. The method of any one of claims 315 to 317, wherein pumping the first target sample from the first sample reservoir into the channel of the flow cell comprises: moving the first target sample from a sample cartridge in the library preparation system using the sipper of the sipper manifold assembly, out an associated pump port of a sample loading assembly, to a corresponding sample port of the sample loading assembly of the sequencing instrument, and into a pump channel fluid line of a pump manifold assembly of the sequencing instrument; and moving the first target sample from the pump channel fluid line through the associated pump port and through a corresponding flow cell port of the sample loading assembly, wherein each flow cell port is coupled to a corresponding port of the flow cell interface and is associated with one of the channels of the plurality of channels of the flow cell.

319. The method of any one of claims 315 to 318, wherein moving the first sample valve of the one or more sample valves to the first position comprises fluidically coupling a sample port of a sample loading assembly of the sequencing instrument, the sipper of the sample sipper assembly, and a corresponding pump of the sequencing instrument, and moving the first sample valve of the one or more sample valves to the second position comprises fluidically coupling the corresponding pump and a channel of the plurality of channels of the flow cell.

320. 320. The method of any one of claims 315 to 319, further comprising operating one or more of a plurality of pumps of the sequencing instrument to individually control fluid flow in each of the plurality of channels of the flow cell.

321. 321. The method of any one of claims 315 to 320, further comprising flowing the first target sample from the first channel of the flow cell into an auxiliary waste line of the sequencing instrument, the auxiliary waste line being upstream of the flow cell and fluidically coupled to a central valve and a waste reservoir of the sequencing instrument.

322. A method according to any one of claims 315 to 321, wherein when the central valve is in a first position, the inlet of the first channel is fluidly coupled to a waste reservoir via the central valve, and the sequencing device comprises the waste reservoir and the central valve.

323. moving the central valve to a second position to fluidly couple a reagent reservoir with the channel and a second channel of the flow cell; pumping a first volume of reagent through the first channel and into the waste reservoir; 323. The method of claim 322, comprising:

324. 1. A method comprising: priming the fluid lines and sample sipper assembly of the library preparation system with read buffer using a pump manifold assembly of the sequencing instrument; drawing a sample of interest from the library preparation system into the fluid lines and into the sequencing instrument using the sample sipper assembly and the pump manifold assembly; drawing a lag buffer into the fluid lines and behind the target sample from the library preparation system and the sequencing instrument using the sample sipper assembly and the pump manifold assembly; forcing the lag buffer, the target sample, and the read buffer toward a channel of a flow cell disposed on a flow cell interface of the sequencing instrument; A method comprising:

325. 325. The method of claim 324, further comprising flowing the lag buffer through the channel of the flow cell before the target sample.

326. 326. The method of any one of claims 324-325, further comprising drawing air bubbles into the fluid line between the read buffer and the sample of interest.

327. 327. The method of any one of claims 324 to 326, further comprising drawing air bubbles into the fluid line between the lag buffer and the target sample.

328. The method of any one of claims 324 to 327, further comprising flowing a disinfectant through the fluid line.

329. 329. The method of claim 328, wherein the disinfectant solution comprises bleach.

330. A method according to any one of claims 324 to 329, wherein the read buffer and the lag buffer form a buffer.

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