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

A system for mapping a plurality of reads of genomic data to genetic reference sequence, using an index of genetic reference data stored in a memory, each read of genomic data representing a sequence of nucleotides, the genetic reference data representing at least a portion of the genetic reference sequence, the system comprising:

• a mapping module formed of a set of a first set of pre-configured hardwired digital logic circuits that are interconnected by a first plurality of physical electrical interconnects, one or more of the first plurality of physical electrical interconnects comprising a memory interface for the mapping module to access the memory, the hardwired digital logic circuits being in a first pre-configured wired configuration to:
• receive a read of genomic data via the memory interface;
• extract a portion of the read to generate a seed, the seed representing a first subset of the sequence of nucleotides represented by the read;
• calculate an address within the index based on the seed;
• access the address in the index in the memory;
• receive a record from the address;
• determine, based on the record, one or more matching positions from the read to the genetic reference sequence;
• and
• output at least one of the matching positions to the memory via the memory interface.

A system for executing a sequence analysis pipeline on a plurality of reads of genomic data using genetic reference data stored in a memory, each read of genomic data representing a sequence of nucleotides, the genetic reference data representing one or more genetic reference sequences, the system comprising:

• an integrated circuit formed of 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 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, the set of processing engines comprising an alignment module in a pre-configured hardwired configuration to:
• receive a plurality of mapped positions for the read from the memory;
• access the memory to retrieve a segment of the genetic reference sequence corresponding to each of the mapped positions;
• calculate an alignment of the read to each retrieved segment of the genetic reference sequence;
• generate a score for each alignment;
• and
• select at least one best-scoring alignment of the read.

A system for executing a sequence analysis pipeline on genetic sequence data, the system comprising:

• an electronic data source that provides digital signals representing a plurality of reads of genomic data, each of the plurality of reads of genomic data comprising a sequence of nucleotides;
• a memory storing one or more genetic reference sequences and an index of the one or more genetic reference sequences;
• and
• an integrated circuit formed of a set of configurable 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 a plurality of steps in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines having:
• a first hardwired configuration to form a mapping module to access, according to at least some of the sequence of nucleotides in a selected read of the plurality of reads, the index of the one or more genetic reference sequences from the memory via the memory interface to map the selected read to one or more segments of the one or more genetic reference sequences based on the index;
• and
• a second hardwired configuration to form an alignment module to access the one or more genetic reference sequences from the memory via the memory interface to align the selected 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.

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 configurable 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 a plurality of steps in the sequence analysis pipeline on the plurality of reads of genomic data, the set of processing engines having:
• a first hardwired configuration to form a mapping module to access, according to at least some of the sequence of nucleotides in a selected read of the plurality of reads, the index of the one or more genetic reference sequences to map the selected read to one or more segments of the one or more genetic reference sequences based on the index;
• and
• a second hardwired configuration to form an alignment module to access the one or more genetic reference sequences to align the selected read to one or more positions in the one or more segments of the one or more genetic reference sequences from the mapping module of the first hardwired configuration;
• 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 configurable 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 of the integrated circuit to:
• configure the configurable hardwired digital logic circuits in a first hardwired configuration;
• access, by the configurable hardwired digital logic circuits in the first hardwired configuration and 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, by the configurable hardwired digital logic circuits in the first hardwired configuration, 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;
• configure the configurable hardwired digital logic circuits in a second hardwired configuration;
• access, by the configurable hardwired digital logic circuits in the second hardwired configuration, the one or more genetic reference sequences from the memory via the memory interface;
• and
• align, by the configurable hardwired digital logic circuits in the second hardwired configuration, the at least one 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 configurable 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 configurable 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 at least one read to one or more positions in the one or more segments of the one or more genetic reference sequences.