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.

What is claimed is: 
     
         1 . A genomics analysis platform for executing a sequence analysis pipeline, the genomics analysis platform comprising:
 one or more of a first integrated circuit, each first integrated circuit forming 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, the CPU having a first set of physical electronic interconnects to connect with a memory;   one or more of a second integrated circuit, each second integrated circuit forming a field programmable gate array (FPGA) having a second set of physical electronic interconnects to connect with the memory, 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; and   a shared memory electronically connected with each CPU and each FPGA via at least a portion of the first and a second set of physical electronic interconnects, respectively, the shared memory being accessible by each CPU and each FPGA to provide genetic sequence data and to store result data from the genomic processing steps performed on the genetic sequence data by each CPU and each FPGA.   
     
     
         2 . The genomics analysis platform in accordance with  claim 1 , wherein the shared memory stores a plurality of reads of genomic data, at least one or more genetic reference sequences, and an index of the one or more genetic reference sequences. 
     
     
         3 . The genomics analysis platform in accordance with  claim 2 , wherein the set of processing engines comprises:
 a mapping module in a first pre-configured hardwired configuration to access, according to at least a portion of a read of the plurality of reads of genomic data, the index of the one or more genetic reference sequences from the shared memory to map the selected read to one or more segments of the one or more genetic reference sequences based on the index.   
     
     
         4 . The genomics analysis platform in accordance with  claim 3 , wherein the first pre-configured hardwired configuration causes the mapping module to:
 receive a read of genomic data via one or more of the plurality of physical electrical interconnects; extract a portion of the read to generate a seed, the seed representing a subset of a sequence of nucleotides represented by the read;   calculate an address within the index based on the seed; access the address in the index in the memory; receive a record from the address, the record representing position information in the genetic reference sequence;   determine one or more matching positions from the read to the genetic reference sequence based on the record; and output at least one of the matching positions to the shared memory.   
     
     
         5 . The genomics analysis platform in accordance with  claim 3 , wherein the set of hardwired digital logic circuits of each FPGA includes:
 a first subset of the hardwired digital logic circuits being configured to receive a read of genomic data via one or more of the plurality of physical electrical interconnects;   a second subset of the hardwired digital logic circuits being configured to extract a portion of the read to generate a seed, the seed representing a subset of the sequence of nucleotides represented by the read;   a third subset of the hardwired digital logic circuits being configured to calculate an address within the index based on the seed;   a fourth subset of the hardwired digital logic circuits being configured to access the address in the index in the memory;   a fifth subset of the hardwired digital logic circuits being configured to receive a record from the address, the record representing position information in the genetic reference sequence; and   a sixth subset of the hardwired digital logic circuits being configured to determine one or more matching positions from the read to the genetic reference sequence based on the record.   
     
     
         6 . The genomics analysis platform in accordance with  claim 5 , wherein each FPGA further includes a set of memory blocks connected with the set of pre-configured hardwired digital logic circuits for temporarily storing the seed, the record, and the one or more matching positions. 
     
     
         7 . The genomics analysis platform in accordance with  claim 3 , wherein the set of processing engines further comprises:
 an alignment module in a second pre-configured hardwired configuration to access the one or more genetic reference sequences from the shared memory to align the portion of the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module.   
     
     
         8 . The genomics analysis platform in accordance with  claim 7 , wherein the second pre-configured hardwired configuration causes the alignment module to:
 receive one or more mapped positions for the read from the mapping module or shared memory;   access the memory to retrieve a segment of the genetic reference sequence corresponding to the matching positions determined by the mapping module;   calculate an alignment of the read to each retrieved genetic reference sequence and generate a score representing the alignment; and select at least one best-scoring alignment of the read.   
     
     
         9 . The genomics analysis platform in accordance with  claim 7 , wherein the set of hardwired digital logic circuits of each FPGA includes:
 a first subset of the hardwired digital logic circuits being configured to receive one or more mapped positions for the read from the mapping module or shared memory;   a second subset of the hardwired digital logic circuits being configured to access the memory to retrieve a segment of the genetic reference sequence corresponding to the matching positions determined by the mapping module;   a third subset of the hardwired digital logic circuits being configured to calculate an alignment of the read to each retrieved genetic reference sequence and generate a score representing the alignment; and a fourth subset of the hardwired digital logic circuits being configured to select at least one best-scoring alignment of the read.   
     
     
         10 . The genomics analysis platform in accordance with  claim 1 , wherein the point-to-point interconnect protocol includes a coherency protocol that ensures coherency among each CPU and each FPGA of the genetic sequence data and result data in the shared memory. 
     
     
         11 . The genomics analysis platform in accordance with  claim 10 , wherein each CPU includes a first cache that stores a first portion of the shared memory and participates in the coherency protocol. 
     
     
         12 . The genomics analysis platform in accordance with  claim 11 , wherein each FPGA includes a second cache that stores a second portion of the shared memory and participates in the coherency protocol. 
     
     
         13 . A genomics analysis platform for executing a sequence analysis pipeline, the genomics analysis platform comprising:
 or more of a first integrated circuit, each first integrated circuit forming 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, the CPU having a first set of physical electronic interconnects for being coupled to a first memory;   one or more of a second integrated circuit, each second integrated circuit forming a field programmable gate array (FPGA) having a second set of physical electronic interconnects to for being coupled to a second memory, 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 genomics 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; and   a first and second memory configured for being electronically coupled with each CPU and each FPGA via at least a portion of the first and second set of physical electronic interconnects, the shared memory being accessible by each CPU and each FPGA to store genetic sequence data and result data from the genomic processing steps performed by each CPU and each FPGA.   
     
     
         14 . The genomics analysis platform in accordance with  claim 13 , where the first and second memories are the same memory. 
     
     
         15 . The genomics analysis platform in accordance with  claim 13 , wherein the shared memory stores a plurality of reads of genomic data, at least one or more genetic reference sequences, and an index of the one or more genetic reference sequences. 
     
     
         16 . The genomics analysis platform in accordance with  claim 15 , wherein the set of processing engines comprises:
 a mapping module in a first pre-configured hardwired configuration to access, according to at least a portion of a read of the plurality of reads of genomic data, the index of the one or more genetic reference sequences from the shared memory to map the selected read to one or more segments of the one or more genetic reference sequences based on the index.   
     
     
         17 . The genomics analysis platform in accordance with  claim 16 , wherein the set of processing engines further comprises:
 an alignment module in a second pre-configured hardwired configuration to access the one or more genetic reference sequences from the shared memory to align the portion of the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module.   
     
     
         18 . The genomics analysis platform in accordance with  claim 13 , wherein each CPU includes a first cache that stores a first portion of the first memory. 
     
     
         19 . The genomics analysis platform in accordance with  claim 18 , wherein each FPGA includes a second cache that stores a second portion of the second memory. 
     
     
         20 . A genomics analysis platform for executing a sequence analysis pipeline, the genomics analysis platform comprising:
 one or more of a first integrated circuit, each first integrated circuit forming 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, the CPU configured for being operably coupled with a memory;   one or more of a second integrated circuit, 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, the FPGA further being configured so as to operably coupled with the memory; and   a shared memory configured for being coupled with each CPU and each FPGA, the shared memory being accessible by each CPU and each FPGA to provide genetic sequence data and to store result data from the genomic processing steps performed on the genetic sequence data by each CPU and each FPGA.