Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform
A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes an integrated circuit formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. The hardwired digital logic circuits are 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 reads of genomic data. In various instances, each subset of the hardwired digital logic circuits may be formed in a wired configuration to perform one or more steps a variant call operation.
1 . A system for executing a Hidden Markov Model (HMM) analysis on genetic sequence data, the genetic sequence data including a read of genomic data and a reference and/or haplotype sequence, the system comprising:
one or more memories for storing the read of genomic sequence data and the reference and/or haplotype sequence, each of the read of genomic sequence data and the reference and/or haplotype sequence comprising a sequence of nucleotides; and
an integrated circuit formed of a plurality of hardwired digital logic circuits that are interconnectable 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 plurality of hardwired digital logic circuits including at least a first subset of hardwired digital logic circuits, the first subset of hardwired digital logic circuits being arranged as a first set of processing engines, a first set of processing engines to perform one or more steps in the HMM analysis on the read of genomic sequence data and the haplotype sequence, the first set of processing engines comprising an HMM module in a first configuration of the subset of hardwired digital logic circuits to access from the one or more memories, via the memory interface, at least some of the sequence of nucleotides in the read of genomic sequence data and the haplotype sequence data, and to perform the HMM analysis on the at least some of the sequence of nucleotides in the read of genomic sequence data and the at least some of the sequence of nucleotides in the haplotype sequence to produce HMM result data; and
one or more of the plurality of physical electrical interconnects comprising an output from the integrated circuit for communicating the HMM result data from the HMM module.