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Genome Biol. 2009;10(11):R134. doi: 10.1186/gb-2009-10-11-r134. Epub 2009 Nov 20.

Searching for SNPs with cloud computing.

Author information

  • 1Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA. blangmea@jhsph.edu

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/.

PMID:
19930550
[PubMed - indexed for MEDLINE]
PMCID:
PMC3091327
Free PMC Article

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