1. An integrated circuit for executing a sequence analysis pipeline on a read of genomic data, derived from a genetic sequence of a subject, using one or more of a reference genetic sequence and a candidate haplotype sequence to determine a probability of observing the read of genomic data assuming the candidate haplotype sequence is a true representation of the subject's genetic sequence, each read of genomic data, the genetic reference sequence, and the candidate haplotype sequence representing a sequence of nucleotides, the integrated circuit being formed of a set of reconfigurable 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 a memory, the reconfigurable hardwired digital logic circuits being arranged as a first set of processing engines, the first set of processing engines to perform a plurality of steps in the sequence analysis pipeline on the read of genomic data and the candidate haplotype sequence, the first set of processing engines comprising a candidate haplotype generation and analysis module in a first hardwired configuration to: receive from the memory, via at least one of the plurality of physical electrical interconnects, a plurality of aligned reads of genomic data; form a pile up out of the plurality of aligned reads of genomic data; generate a graph of potential candidate haplotype sequences from the pile up of reads of genomic data to produce a generated graph; extract a candidate haplotype sequence from the generated graph of potential haplotype sequences to produce an extracted contiguous candidate haplotype sequence; select a read of genomic data for sequence analysis; compare the sequence of nucleotides of the contiguous candidate haplotype sequence to the sequence of nucleotides of the read of genomic data; perform a Hidden Markov Model (HMM) operation on each of the nucleotide sequences of the read of genomic data and the contiguous candidate haplotype sequence; and determine a probability of observing the read of genomic data assuming the candidate haplotype sequence is a true representation of the subject's genetic sequence.