Bioinformatics Systems, Apparatuses, and Methods Executed on an Integrated Circuit Processing Platform

A structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data from 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, and using a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences, the structured ASIC comprising:

• a master slice that includes a set of digital logic circuits;
• and
• one or more configurable metal layers formed on the master slice, each of the one or more configurable metal layers having a set of wired connections, the wired connections of the one or more configurable metal layers being arranged to interconnect a subset of the digital logic circuits to form a set of processing engines, the set of processing engines comprising:
• a mapping engine to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index;
• and
• an alignment engine to access the one or more genetic reference sequences from the memory 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 engine.

A method of making a structured application-specific integrated circuit (ASIC) for analyzing genetic sequence data, the method comprising:

• providing a plurality of photolithographic masks that define a set of digital logic circuits of the structured ASIC;
• forming the set of digital logic circuits using the plurality of photolithographic masks to form a first master slice and a second master slice that is equivalent to the first master slice;
• providing a first set of configurable metal layer masks that define a first digital logic configuration;
• forming a first set of configurable metal layers onto the first master slice using the first set of configurable metal layer masks, the first set of configurable metal layers having a set of wired connections arranged according to the first set of configurable metal layer masks to interconnect a subset of the digital logic circuits of the first master slice according to the first digital logic configuration;
• providing a second set of configurable metal layer masks that define a second digital logic configuration;
• forming a second set of configurable metal layers onto the second master slice using the second set of configurable metal layer masks, the second set of configurable metal layers having a set of wired connections arranged according to the second set of configurable metal layer masks to interconnect a subset of the digital logic circuits of the second master slice according to the second digital logic configuration;
• the first digital logic configuration including an input for connecting to 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, the first digital logic configuration further including a memory interface to a memory storing one or more genetic reference sequences associated with genomic data and an index of the one or more genetic reference sequences;
• and
• the first digital logic configuration further including a set of processing engines, the set of processing engines comprising a mapping engine to access the index of the one or more genetic reference sequences from the memory to map the read to one or more segments of the one or more genetic reference sequences based on the index.