Faster and More Accurate Sequence Alignment with SNAP

TL;DR

SNAP is a new sequence aligner that is significantly faster and more accurate than existing tools, using a hash-based indexing approach and optimized local alignment checks to handle long reads and complex mutations efficiently.

Contribution

SNAP introduces a hash-based alignment method that improves speed and accuracy over BWA, especially for long reads and complex mutations.

Findings

SNAP aligns a human genome dataset in under an hour at low cost.

SNAP achieves higher accuracy than BWA in read alignment.

SNAP scales well for long reads from hundreds to thousands of bases.

Abstract

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer 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 a simple hash index of short seed sequences from the genome, similar to BLAST's. However, SNAP greatly reduces the number and cost of local alignment checks performed through several measures: it uses longer seeds to reduce the false positive 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 result 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 30x 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.