Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

A genomics analysis platform for executing a sequence analysis pipeline on a plurality of reads of genomic data, 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 configurable 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;
• 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 at least one CPU via a portion of the first set of physical electronic interconnects using a point-to-point interconnect, 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, wherein the set of processing engines further comprise:
• an alignment module in a configurable hardwired configuration to access one or more genetic reference sequences from a shared memory to align a portion of a selected read of the plurality of reads of genomic data to one or more positions in one or more segments of one or more genetic reference sequences;
• and
• the shared memory being electronically connected with each CPU and each FPGA via at least a portion of the first 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, wherein the shared memory stores the plurality of reads of genomic data, at least one or more genetic reference sequences, and the index of the one or more genetic reference sequences;
• the point-to-point interconnect implementing a coherency protocol that ensures coherency among each CPU and each FPGA of the data in the shared memory.

A system for executing a sequence analysis pipeline on a plurality of reads of genomic data using an index of genetic reference data stored in a memory, each read of genomic data representing a sequence of nucleotides, the genetic reference data representing one or more genetic reference sequences, the system comprising:

• an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, one or more of the plurality of physical electrical interconnects comprising a memory interface for the integrated circuit to access the memory, the hardwired digital logic circuits being arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired digital logic circuits to perform one or more steps in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines having a hardwired configuration 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 the 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 memory via the memory interface.

An integrated circuit for mapping, using an index of genetic reference data stored in a memory, a plurality of reads of genomic data to one or more genetic reference sequences represented by the genetic reference data, each read of genomic data comprising a sequence of nucleotides, the integrated circuit comprising:

• a set of configurable hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects;
• the set of configurable hardwired digital logic circuits comprising:
• a first subset of the configurable 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 configurable 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 configurable hardwired digital logic circuits being configured to calculate an address within the index based on the seed;
• a fourth subset of the configurable hardwired digital logic circuits being configured to access the address in the index in the memory;
• a fifth subset of the configurable hardwired digital logic circuits being configured to receive a record from the address, the record representing position information in the genetic reference sequence;
• a sixth subset of the configurable 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;
• a set of memory blocks connected with the set of configurable hardwired digital logic circuits for temporarily storing the seed, the record, and the one or more matching positions;
• and
• an output formed of a second subset of the plurality of physical electrical interconnects for outputting at least one of the matching positions.