1. An integrated circuit for executing a sequence analysis pipeline on genetic sequence data including a plurality of reads of genomic data and reference sequence data from an external data source, each read of genomic data and the reference sequence data comprising a sequence of nucleotides, the integrated circuit comprising: a set of pre-configured 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 an interface for the integrated circuit to access the plurality of reads of genomic data and the reference sequence data from the external data source, 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 a variant calling operation in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines comprising a variant calling module in a first pre-configured wired configuration to access the plurality of reads and the reference sequence data, compare the nucleotides in the plurality of reads to the nucleotides of the reference sequence data to determine one or more differences between the sequences of nucleotides in the plurality of reads and the sequence of nucleotides in the reference sequence data, and generate one or more variant calls representing the one or more differences.