Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform

A system for executing a sequence analysis pipeline on a plurality of reads of genomic data, one or more genetic reference sequences, and an index of the one or more genetic reference sequences, each read of genomic data comprising a sequence of nucleotides, the system comprising:

• 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 an input to the integrated circuit connected with the electronic data source for receiving the plurality of reads of genomic data, one or more of the plurality of physical electrical interconnects further 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 data, each subset of the hardwired digital logic circuits being in a wired configuration to perform the one or more steps in the sequence analysis pipeline, 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 to map the read to one or more segments of the one or more genetic reference sequences based on the index;
• and
• an alignment module in the wired configuration to access the one or more genetic reference sequences to align the read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module;
• 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 and/or the alignment module.

An apparatus for executing a sequence analysis pipeline on genetic sequence data, the genetic sequence data comprising one or more genetic reference sequences and one or more reads of genomic data, the apparatus comprising:

• a memory storing the one or more genetic reference sequences and an index of the one or more genetic reference sequences;
• and
• an integrated circuit comprising a set of hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, at least one of the plurality of physical electrical interconnects comprising an input for receiving the one or more reads of genomic data, at least one of the plurality of physical electrical interconnects comprising a memory interface for the integrated circuit to access the memory, and at least one of the plurality of physical electrical interconnects comprising an output for providing result data, the set of hardwired digital logic circuits being in a wired configuration to:
• access, according to at least some of the sequence of nucleotides in at least one read of the one or more reads of genomic data, the index of the one or more genetic reference sequences from the memory via the memory interface;
• map the at least one read of the one or more reads of genomic data to one or more segments of the one or more genetic reference sequences based on the index;
• access the one or more genetic reference sequences from the memory via the memory interface;
• and
• align the read to one or more positions in the one or more segments of the one or more genetic reference sequences.

An apparatus for executing a sequence analysis pipeline on genetic sequence data, the genetic sequence data comprising one or more genetic reference sequences and one or more reads of genomic data, the apparatus comprising:

• an integrated circuit comprising a set of hardwired digital logic circuits that are interconnected by a plurality of physical electrical interconnects, at least one of the plurality of physical electrical interconnects comprising an input for receiving the one or more reads of genomic data and at least one of the plurality of physical electrical interconnects comprising an output for providing result data, the set of hardwired digital logic circuits being in a wired configuration to:
• store the one or more genetic reference sequences in a memory associated with the integrated circuit;
• store an index of the one or more genetic reference sequences in the memory;
• access, according to at least some of the sequence of nucleotides in at least one read of the one or more reads of genomic data, the index of the one or more genetic reference sequences from the memory via one or more of the plurality of physical electrical interconnects;
• map the at least one read of the one or more reads of genomic data to one or more segments of the one or more genetic reference sequences based on the index;
• access the one or more genetic reference sequences from the memory via one or more of the plurality of physical electrical interconnects;
• and
• align the read to one or more positions in the one or more segments of the one or more genetic reference sequences.