METHODS AND SYSTEMS FOR QUANTIFYING SEQUENCE ALIGNMENT

摘要

The invention includes methods for aligning reads (e.g., nucleic acid reads, amino acid reads) to a reference sequence construct, methods for building the reference sequence construct, and systems that use the alignment methods and constructs to produce sequences. The invention also includes methods and systems for evaluating the quality of the alignment between the reads and the reference sequence construct. The method is scalable, and can be used to align millions of reads to a construct thousands of bases or amino acids long. The invention additionally includes methods for identifying a disease or a genotype based upon alignment of nucleic acid reads to a location in the construct.

主权项

1. A system for quantifying an alignment between a sequence read and a reference sequence construct, the system comprising a computer processor and memory, the memory including instructions that, when executed, cause the processor to:
obtain a sequence read; align the sequence read to a reference sequence construct comprising a first portion to which the read aligns and either a first alternative portion or a second alternative portion; determine the number of overlapping bases or amino acids between the sequence read and the first portion and between the sequence read and the first alternative portion or the second alternative portion; and identify a smallest number of overlapping bases or amino acids, thereby quantifying the alignment between the sequence read and the reference sequence construct.