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 a sequence analysis pipeline platform connected with the memory via a memory interface, the sequence analysis pipeline platform comprising: a mapping module formed of a first set of hardwired digital logic circuits in a first configuration 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 formed of a second set of hardwired digital logic circuits in a second configuration 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 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 an output formed of one or more physical electrical interconnects from the sequence analysis pipeline platform for communicating result data from the mapping module and/or the alignment module and/or variant calling module.