Software

Searching for SNPs with cloud computing

Ben Langmead^1,2 , Michael C Schatz² , Jimmy Lin³ , Mihai Pop² and Steven L Salzberg²

¹  Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA

²  Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA

³  The iSchool, College of Information Studies, University of Maryland, College Park, MD 20742, USA

author email corresponding author email

Genome Biology 2009, 10:R134doi:10.1186/gb-2009-10-11-r134

Published:	20 November 2009

Subject areas: Bioinformatics, Genome studies

Abstract

As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the SNP caller SOAPsnp. Executing in parallel using Hadoop, Crossbow analyzes data comprising 38-fold coverage of the human genome in three hours using a 320-CPU cluster rented from a cloud computing service for about $85. Crossbow is available from http://bowtie-bio.sourceforge.net/crossbow/ webcite.