Bioinformatics Systems, Apparatuses, And Methods Executed On An Integrated Circuit Processing Platform

摘要

A system, method and apparatus for executing a sequence analysis pipeline on genetic sequence data includes a structured ASIC formed of a set of hardwired digital logic circuits that are interconnected by physical electrical interconnects. One of the physical electrical interconnects forms an input to the structured ASIC connected with an electronic data source for receiving reads of genomic data. The hardwired digital logic circuits are 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 reads of genomic data. Each subset of the hardwired digital logic circuits is formed in a wired configuration to perform the one or more steps in the sequence analysis pipeline.

主权项

1. A system for analyzing genetic sequence data, the system comprising:
a memory, the memory comprising one or more genetic reference sequences and an index of the one or more genetic reference sequences; a structured application specific integrated circuit (ASIC) comprising a plurality of mask-programmed, hardwired digital logic circuits mask-configured as a plurality of processing engines comprising a mapping module and an alignment module, and a plurality of physical electrical interconnects comprising an input to the structured ASIC, a memory interface for the structured ASIC, and an output from the structured ASIC; wherein the input to the structured ASIC is connectable to an electronic data source to receive the plurality of reads of genomic data; wherein the memory interface for the structured ASIC is configured to access the memory; wherein the mapping module is configured to access the index of the one or more genetic reference sequences from the memory via the memory interface and configured to map a read to one or more segments of the one or more genetic reference sequences based on the index of the one or more genetic reference sequences; wherein the alignment module is configured to access the one or more genetic reference sequences from the memory via the memory interface 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 wherein the output from the structured ASIC is configured to communicate result data from the mapping module and/or the alignment module.