Systems and methods for sequence data alignment quality assessment

A method for classifying alignments of paired nucleic acid sequence reads, comprising:

• receiving, by a computing device comprising a processor and memory, a plurality of paired nucleic acid sequence reads, wherein each paired nucleic acid sequence read comprises a first read of a first tag derived from a first region of a polynucleotide and a second read of a second tag derived from a second region of the polynucleotide, the first and second reads produced by next generation sequencing, wherein the first tag and the second tag are separated by an insert region;
• mapping, by the computing device, the first and second reads of each paired nucleic acid sequence read to a reference genome to form potential alignments, wherein one or more potential alignments are produced for each paired nucleic acid sequence read, wherein each potential alignment satisfies a minimum threshold mismatch constraint;
• identifying, by the computing device, potential paired alignments of the first and second reads of each 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;
• 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;
• and
• selecting, by the computing device, the potential paired alignment having a highest alignment score as a primary alignment for each paired nucleic acid sequence read.

A system for sequence alignment quality assessment, comprising:

• a next generation sequencing instrument configured to interrogate a sample to produce a plurality of read sequences from the sample;
• and
• a processor in communication with the next generation sequencing instrument, the processor configured to,
• obtain the read sequences from the next generation sequencing instrument,
• map the read sequences to a reference genome to produce potential alignments, wherein one or more potential alignments are produced for a given read sequence, wherein each potential alignment satisfies a minimum threshold mismatch constraint,
• calculate a quality value for each potential alignment,
• output the potential alignments and associated quality values, and
• select the potential alignment having a highest quality value as a primary alignment for the given read sequence.

A method for sequence alignment quality assessment, comprising:

• interrogating a sample, by a next generation sequencing instrument, to produce a plurality of read sequences from the sample;
• obtaining, by a computing device comprising a processor and a memory, the plurality of read sequences from the next generation sequencing instrument;
• mapping, by the computing device, the read sequences to a reference genome to produce potential alignments, wherein one or more potential alignments are produced for a given read sequence, wherein each potential alignment satisfies a minimum threshold mismatch constraint;
• calculating, by the computing device, a quality value for each potential alignment;
• outputting, by the computing device, the potential alignments and associated quality values;
• and
• selecting, by the computing device, the potential alignment having a highest quality value as a primary alignment.