Bioinformatics Systems, Apparatuses, and Methods Executed on a Quantum Processing Platform

Abstract

A system, method and apparatus for executing a bioinformatics analysis on genetic sequence data includes a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits. The hardwired quantum logic circuits may be arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum logic circuits to perform one or more steps in the bioinformatics analysis on the reads of genomic data. Each subset of the hardwired quantum logic circuits may be formed in a wired configuration to perform the one or more steps in the bioinformatics analysis.

What is claimed is: 
     
         1 . A system for executing a sequence analysis pipeline on a plurality of reads of genomic data 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 one or more genetic reference sequences, the system comprising:
 a quantum computing device formed of a set of hardwired quantum logic circuits interconnected by a plurality of superconducting connections to process information represented as a quantum state that is configured as a set of one or more qubits, one or more of the plurality of superconducting connections comprising a memory interface for accessing the memory, the set of hardwired quantum logic circuits being arranged as a set of processing engines, each processing engine being formed of a subset of the hardwired quantum 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 a mapping module in a first hardwired configuration to:
 receive a read of genomic data via the memory interface of the one or more of the plurality of superconducting connections; 
 extract a portion of the read to generate a seed, the seed representing a subset of the sequence of nucleotides represented by the read; 
 calculate a first address within the index based on the seed; 
 access the address in the index in the memory; 
 receive a record from the address, the record representing position information in the genetic reference sequence; 
 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.