Patent Document ID: 9268903
Application ID: 13177267
Patent Status: 1

Claim One:
1. A method for classifying alignments of paired nucleic acid sequence reads, comprising: disposing a nucleic acid sample within a sample chamber of a sequencing instrument, the nucleic acid sample comprising a plurality of target nucleic acids, the target nucleic acids including first and second tags, the first tag being derived from a first region of a polynucleotide and the second tag being derived from a second region of the polynucleotide, the first and second tags being separated by an insert region; detecting, by a detection device, a plurality of signals representative of the sequence of at least one of the target nucleic acids of the nucleic acid sample; generating, by a computing device comprising a processor and memory, a paired nucleic acid sequence read from the plurality of signals, the paired nucleic acid sequence read including a first read of the first tag and second read of the second tag; determining, by the computing device, potential alignments for the first and second reads of the paired nucleic acid sequence read to a reference sequence, wherein each potential alignment satisfies a minimum threshold mismatch constraint; identifying, by the computing device, potential paired alignments of the paired nucleic acid sequence read, wherein a distance between the first and second reads of each potential paired alignment is within an estimated insert size range; and calculating, by the computing device, an alignment score for each potential paired alignment based on: a distance between the first and second reads, and a total number of mismatches for the first and second reads.