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Searching for SNPs with cloud computing
Ben Langmead (Johns Hopkins University, University of Maryland, College Park), Michael C. Schatz (University of Maryland, College Park), Jimmy Lin (University of Maryland, College Park), Mihai Pop (University of Maryland, College Park), Steven L. Salzberg (University of Maryland, College Park)
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/.