Incremental Nucleic Acid Secondary Analysis With FPGA Mapping
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Solution Overview
Problem
Conventional nucleic acid sequencers face inefficiencies due to the lack of computational resources to perform primary and secondary analysis operations in parallel, leading to prolonged downtime, reduced throughput, and increased reagent consumption, with tertiary analysis often taking days to commence.
Innovation Solution
Offloading secondary analysis operations to a programmable logic unit with hardwired digital logic, allowing parallel execution of sequencing and secondary analysis tasks, such as mapping and aligning, using hardware circuits.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Loss of time
If secondary analysis operations are performed sequentially after primary analysis completion, then computational resources are sufficient for accurate processing, but processing time is prolonged and instrument downtime increases
Solution Approach 1:
The patent segments the analysis workflow into primary analysis and secondary analysis as separate functional modules. The mapping and alignment unit is implemented as a distinct hardware component (FPGA or ASIC) that operates independently from the main sequencing computational resources, allowing parallel execution without overwhelming any single computational subsystem
Solution Approach 2:
The patent introduces a mapping and alignment unit as an intermediary hardware component between the sequencer and tertiary analysis software. This unit pre-processes sequencing data by performing mapping and alignment operations, delivering pre-processed data to tertiary analysis tools, thereby enabling parallel operation while maintaining data quality
2Productivity
If computational resources are allocated for parallel primary and secondary analysis, then throughput increases, but device complexity and resource requirements increase
Solution Approach 1:
The patent replaces software-based secondary analysis operations with hardware-based mapping and alignment units (FPGA or ASIC). This substitution enables parallel processing of primary and secondary analysis tasks simultaneously, dramatically improving throughput while the hardware units handle the computational burden independently
Solution Approach 2:
The patent creates a dedicated mapping and alignment unit that copies the essential functionality of secondary analysis operations. This hardware copy performs mapping and alignment in parallel with sequencing, eliminating the need for sequential processing and thereby increasing overall instrument throughput
3Loss of substance
If sequential processing is used to simplify device architecture, then device complexity is reduced, but reagent consumption increases due to prolonged processing time
Solution Approach 1:
The patent enables continuous operation by allowing secondary analysis (mapping and alignment) to proceed in parallel with primary analysis (sequencing). The mapping and alignment unit processes data continuously as it is generated, eliminating idle time and reducing the overall duration of the sequencing run, thereby reducing reagent consumption
Data Source
AI summary
Methods, systems, and apparatuses, including computer programs, for performing incremental secondary analysis of nucleic acid sequence reads. The method can include (i) obtaining first data describing a plurality of first reads generated by a nucleic acid sequencing device during a first read interval, (ii) obtaining second data describing a plurality of second reads generated by the nucleic acid sequencing device during a second read interval that is performed after the first read interval, wherein while the second data is being obtained: (a) providing, by the nucleic acid sequencing device, the first data as an input to a mapping and alignment unit, (b) receiving, from the mapping and alignment unit, alignment results, and (c) storing the received alignment results, and, thereafter (iii) instructing the mapping and alignment unit to begin alignment of the second data representing the second plurality of reads to the reference sequence.