1. A system for executing a sequence analysis pipeline on genetic sequence data, the system comprising: a memory for storing one or more genetic reference sequences, an index of the one or more genetic reference sequences, and a plurality of reads of genomic data, each of the genetic reference sequences and the plurality of reads of genomic data comprising a sequence of nucleotides; and 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 at least one step in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines comprising: a mapping module in a first configuration of the hardwired digital logic circuits to access in the memory, via the memory interface, at least some of the sequence of nucleotides in a selected read of the plurality of reads and the index of the one or more genetic reference sequences, and to map the selected read to one or more segments of the one or more genetic reference sequences based on the index to produce a mapped read; an alignment module in a second configuration of the hardwired digital logic circuits to access the one or more genetic reference sequences from the memory via the memory interface to align the mapped read from the mapping module to one or more positions in the one or more segments of the one or more genetic reference sequences to produce an aligned read; and a variant calling module in a third configuration of the hardwired digital logic circuits to access the aligned read and at least one of the genetic reference sequences, compare the sequence of nucleotides in the aligned reads to the sequence of nucleotides of the at least one genetic reference sequence, to determine one or more differences between the sequence of nucleotides in the aligned read and the sequence of nucleotides in the at least one genetic reference sequence, and to generate one or more variant calls representing the one or more differences; and one or more of the plurality of physical electrical interconnects comprising an output from the integrated circuit for communicating result data from the mapping module and/or the alignment module and/or variant calling module.