Bioinformatics systems, apparatus, and methods for performing secondary and/or tertiary processing

Abstract

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data is provided. Particularly, a genomics analysis platform for executing a sequence analysis pipeline is provided. The genomics analysis platform includes one or more of a first integrated circuit, where each first integrated circuit forms a central processing unit(CPU) that is responsive to one or more software algorithms that are configured to instruct the CPU to perform a first set of genomic processing steps of the sequence analysis pipeline. Additionally, a second integrated circuit is also provided, where each second integrated circuit forming a field programmable gate array (FPGA), the FPGA being configured by firmware to arrange a set of hardwired digital logic circuits that are interconnected by a plurality of physical interconnects to perform a second set of genomic processing steps of the sequence analysis pipeline, the set of hardwired digital logic circuits of each FPGA being arranged as a set of processing engines to perform the second set of genomic processing steps. A shared memory is also provided.

Description

[0001] Cross References to Related Applications [0002] This application asserts the priority date of the following patent applications: [0003] U.S. Patent Application No. 63 / 347,080 filed June 7, 2016; [0004] U.S. Patent Application No. 62 / 399,582 filed September 26, 2016; [0005] U.S. Patent Application No. 62 / 414,637 filed October 28, 2016; [0006] U.S. Patent Application No. 15 / 404,146 filed January 11, 2017; [0007] U.S. Patent Application No. 62 / 462,869 filed February 23, 2017; [0008] U.S. Patent Application No. 62 / 469,442 filed March 9, 2017; [0009] U.S. Patent Application No. 15 / 497,149 filed April 25, 2017; [0010] The entire disclosure of each application is incorporated herein by reference. technical field [0011] The subject matter described in this disclosure relates to bioinformatics, and more particularly to a system, apparatus, and method for implementing a bioinformatics solution, such as one or more function. Background technique [00...

AI Technical Summary

Problems solved by technology

[0013] Keeping pace with such increased sequencing throughput generated by Next Gen Sequencers typically manifests itself as multi-threaded software tools that are already executing on a greater number of faster processors in computer clusters, These processors require large amounts of power, significant IT support costs, and expensive high-availability memory

Importantly, future improvements in throughput sequencing speed for secondary processing solutions translate into increased real dollar costs of acceleration

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