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; 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 to perform steps 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, the mapping module comprising: a first subset of the first configuration of the hardwired digital logic circuits that is configured to receive a read of genomic data via one or more of the plurality of physical electrical interconnects; a second subset of the first configuration of the hardwired digital logic circuits that is configured to extract a portion of the read to generate a seed, the seed representing a subset of the sequence of nucleotides represented by the read; a third subset of the first configuration of the hardwired digital logic circuits that is configured to calculate an address within the index based on the seed; a fourth subset of the first configuration of the hardwired digital logic circuits that is configured to access the address in the index in the memory; a fifth subset of the first configuration of the hardwired digital logic circuits that is configured to receive a record from the address, the record representing position information in the genetic reference sequence; and a sixth subset of the first configuration of the hardwired digital logic circuits that is configured to determine one or more matching positions from the read to the genetic reference sequence based on the record, so as to produce mapped positions for the read; and an alignment module in a second configuration of the hardwired digital logic circuits, the alignment module comprising: a first subset of the second configuration of the hardwired digital logic circuits that is configured to receive one or more of the mapped positions for the read from the memory; a second subset of the second configuration of the hardwired digital logic circuits that is configured to access the memory to retrieve a segment of the genetic reference sequence corresponding to each of the mapped positions; a third subset of the second configuration of the hardwired digital logic circuits that is configured to calculate an alignment of the read to each retrieved segment of the genetic reference sequence; a fourth subset of the second configuration of the hardwired digital logic circuits that is configured to generate a score for each alignment; and a fifth subset of the second configuration of the hardwired digital logic circuits that is configured to select at least one best-scoring alignment of the read; and an output formed of a subset of the plurality of physical electrical interconnects for outputting the best-scoring alignment of the read.