Bioinformatics systems, apparatuses, 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

CROSS REFERENCE TO RELATED APPLICATION[0001]This application claims priority under 35 U.S.C. §119(e) to U.S. Provisional Application Ser. No. 62 / 347,080, filed Jun. 7, 2016, entitled “Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform”; to U.S. Provisional Application Ser. No. 62 / 399,582, filed Sep. 26, 2016, entitled “Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform”, U.S. Provisional Application Ser. No. 62 / 414,637, filed Oct. 28, 2016, entitled “Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform”; to U.S. Provisional Application Ser. No. 62 / 462,869, filed Feb. 23, 2017, entitled “Bioinformatics Systems, Apparatuses, and Methods Executed on a Quantum Processing Platform”; to U.S. Provisional Application Ser. No. 62 / 469,442, filed Mar. 9, 2017, entitled “Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrate...

AI Technical Summary

Benefits of technology

The present patent is about devices, systems, and methods for performing genomics and bioinformatics protocols on data generated through a primary processing procedure, such as genetic sequencing. The devices and systems provide faster processing speed, better accuracy, and enhanced overall efficiency compared to standard secondary processing pipelines. The system includes a novel variant call module that can perform improved variant call functions. The system also optimizes processing speed and accuracy on a wide range of sequence data sets. The devices and systems can be implemented in software or hardware, or a combination of both. The patent also describes a system for sharing memory resources amongst the components of the system. Overall, the patent provides faster, more accurate, and efficient tools for genomics and bioinformatics analysis.

Problems solved by technology

As described in detail herein, some major computational challenges for high-throughput DNA sequencing analysis is to address the explosive growth in available genomic data, the need for increased accuracy and sensitivity when gathering that data, and the need for fast, efficient, and accurate computational tools when performing analysis on a wide range of sequencing data sets derived from such genomic data.

Keeping pace with such increased sequencing throughput generated by Next Gen Sequencers has typically been manifested as multithreaded software tools that have been executed on ever greater numbers of faster processors in computer clusters with expensive high availability storage that requires substantial power and significant IT support costs.

Importantly, future increases in sequencing throughput rates will translate into accelerating real dollar costs for these secondary processing solutions.

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