1. A system for executing a sequence analysis pipeline on genetic sequence data, the system comprising: a memory storing one or more genetic reference sequences, an index of the one or more genetic reference sequences, and a plurality of reads of genomic sequence data, each of the one or more genetic reference sequences and the plurality of reads of genomic sequence data comprising a sequence of nucleotides; and an integrated circuit formed 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 sequence data, the set of processing engines comprising: a mapping module in the wired configuration to access, according to at least some of the sequence of nucleotides in a read of the plurality of reads, the index of the one or more genetic reference sequences from the memory via the memory interface to map the read to one or more segments of the one or more genetic reference sequences based on the index to produce a mapped read; 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.