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We present the Scalable Nucleotide Alignment Program (SNAP), a new short andlong read aligner that is both more accurate (i.e., aligns more reads withfewer errors) and 10-100x faster than state-of-the-art tools such as BWA.Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses asimple hash index of short seed sequences from the genome, similar to BLAST's.However, SNAP greatly reduces the number and cost of local alignment checksperformed through several measures: it uses longer seeds to reduce the falsepositive locations considered, leverages larger memory capacities to speedindex lookup, and excludes most candidate locations without fully computingtheir edit distance to the read. The result is an algorithm that scales wellfor reads from one hundred to thousands of bases long and provides a rich errormodel that can match classes of mutations (e.g., longer indels) that today'sfast aligners ignore. We calculate that SNAP can align a dataset with 30xcoverage 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 furtherimprove SNAP.

Faster and More Accurate Sequence Alignment with SNAP