The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.

ABSTRACT: Read alignment is an ongoing challenge for the analysis of data from sequencing technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and-vote, for mapping reads to a reference genome. The new strategy chooses the mapped genomic location for the read directly from the seeds. It uses a relatively large number of short seeds (called subreads) extracted from each read and allows all the seeds to vote on the optimal location. When the read length is <160 bp, overlapping subreads are used. More conventional alignment algorithms are then used to fill in detailed mismatch and indel information between the subreads that make up the winning voting block. The strategy is fast because the overall genomic location has already been chosen before the detailed alignment

SUBMITTER: Liao Y 

PROVIDER: S-EPMC3664803 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature