Searching for SNPs with cloud computing
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
Genome Biology 2009, 10:R134 doi:10.1186/gb-2009-10-11-r134Published: 20 November 2009
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.