MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence.

ABSTRACT:

Background

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it can take hours and days to map millions of reads even for bacteria genomes.

Results

We introduce a GPU program called MaxSSmap with the aim of achieving comparable accuracy to Smith-Waterman but with faster runtimes. Similar to most programs MaxSSmap identifies a local region of the genome followed by exact alignment. Instead of using hash tables or Burrows-Wheeler in the first part, MaxSSmap calculates maximum scoring subsequence score between the read and disjoint fragments of the genome in parallel on a GPU and selects the hig

SUBMITTER: Turki T 

PROVIDER: S-EPMC4289234 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature