Faster and More Accurate Sequence Alignment with SNAP

TitleFaster and More Accurate Sequence Alignment with SNAP
Publication TypeMiscellaneous
Year of Publication2011
AuthorsZaharia, M., Bolosky W. J., Curtis K., Fox A., Patterson D., Shenker S., Stoica I., Karp R. M., & Sittler T.
Other Numbers3256

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 10–100faster than state-of-the-art tools such as BWA. Unlike recentaligners based on the Burrows-Wheeler transform, SNAP usesa simple hash index of short seed sequences from the genome,similar to BLAST’s. However, SNAP greatly reduces the numberand cost of local alignment checks performed through severalmeasures: it uses longer seeds to reduce the false positivelocations considered, leverages larger memory capacitiesto speed index lookup, and excludes most candidate locationswithout fully computing their edit distance to the read. The resultis an algorithm that scales well for reads from one hundredto thousands of bases long and provides a rich error model thatcan match classes of mutations (e.g., longer indels) that today’sfast aligners ignore. We calculate that SNAP can align a datasetwith 30 coverage of a human genome in less than an hour fora cost of $2 on Amazon EC2, with higher accuracy than BWA.Finally, we describe ongoing work to further improve SNAP.


We would like to thank Matthew Meyerson for providingmotivation and encouragement for this work, and forhis feedback on its utility in cancer and pathogen discovery.This research is supported in part by gifts fromthe following Berkeley AMP Lab sponsors: Google,SAP, Amazon Web Services, Cloudera, Ericsson, GeneralElectric, Huawei, IBM, Intel, Mark Logic, Microsoft,NEC Labs, Network Appliance, Oracle, QuantaComputer, Splunk and VMware, and by DARPA (contract#FA8650-11-C-7136).

Bibliographic Notes under arXiv:1111.5572v1

Abbreviated Authors

M. Zaharia, W. J. Bolosky, K. Curtis, A. Fox, D. Patterson, S. Shenker, I. Stoica, R. M. Karp, and T. Sittler

ICSI Research Group


ICSI Publication Type