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Searching for SNPs with cloud computing

Ben Langmead12*, Michael C Schatz2, Jimmy Lin3, Mihai Pop2 and Steven L Salzberg2

Author Affiliations

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

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Genome Biology 2009, 10:R134  doi:10.1186/gb-2009-10-11-r134

Published: 20 November 2009

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.