1. A system for executing a Hidden Markov Model (HMM) analysis on genomic sequence data, the genomic sequence data including a read of genomic data and a candidate haplotype sequence, both the read of genomic sequence data and the candidate haplotype sequence comprising a sequence of nucleotides, the system comprising: one or more memories for storing the read of genomic sequence data and the candidate haplotype sequence; 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 the hardwired digital logic circuits, the first subset of the hardwired digital logic circuits being arranged as a first set of processing engines, the first set of processing engines comprising a first subset of processing engines to perform one or more steps in an HMM analysis on the read of genomic sequence data and the candidate haplotype sequence, the first subset of processing engines comprising an HMM module to access from the one or more memories, via the memory interface the read of genomic sequence data and the candidate haplotype sequence, to compare the nucleotides in the read of genomic data to the sequence of nucleotides in the candidate haplotype sequence, and to perform the HMM analysis on at least some of the sequence of nucleotides in the read of genomic sequence data and at least some of the sequence of nucleotides in the candidate haplotype sequence to produce HMM result data, the HMM result data comprising a probability that the candidate haplotype sequence represents the true genetic sequence of a subject; 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.