Faster and More Accurate Sequence Alignment with SNAP

Matei Zaharia, William J. Bolosky, Kristal Curtis, Armando Fox, David Patterson, Scott Shenker, Ion Stoica, Richard M. Karp, and Taylor Sittler

Abstract

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more ac- curate (i.e., aligns more reads with fewer errors) and 10–100× faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST’s. However, SNAP greatly reduces the num- ber and cost of local alignment checks performed through sev- eral measures: it uses longer seeds to reduce the false posi- tive locations considered, leverages larger memory capacities to speed index lookup, and excludes most candidate locations without fully computing their edit distance to the read. The re- sult is an algorithm that scales well for reads from one hundred to thousands of bases long and provides a rich error model that can match classes of mutations (e.g., longer indels) that today’s fast aligners ignore. We calculate that SNAP can align a dataset with 30× coverage of a human genome in less than an hour for a cost of $2 on Amazon EC2, with higher accuracy than BWA. Finally, we describe ongoing work to further improve SNAP.

Details

Publication typeArticle
Published inarXiv
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