1. An apparatus for executing one or more steps of a sequence analysis pipeline on genetic data, the genetic data comprising one or more genetic reference sequences, an index of the one or more genetic reference sequences, and a plurality of reads of genomic data, the apparatus comprising: an integrated circuit comprising 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 an input for receiving the plurality of reads of genomic data, the set of reconfigurable hardwired digital logic circuits being in a wired configuration to access the index of the one or more genetic reference sequences via one of the plurality of physical electrical interconnects, and to map the plurality of reads of genomic data to one or more segments of the one or more genetic reference sequences according to the index.