Searching for SNPs with cloud computing

Ben Langmead, Michael C. Schatz, Jimmy Lin, Mihai Pop, Steven L. Salzberg

Research output: Contribution to journalArticle

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/.

Original languageEnglish (US)
Article numberR134
JournalGenome biology
Volume10
Issue number11
DOIs
StatePublished - Nov 20 2009

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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