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Searching for SNPs with cloud computing.

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/.

SUBMITTER: Langmead B 

PROVIDER: S-EPMC3091327 | biostudies-other | 2009

REPOSITORIES: biostudies-other

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Searching for SNPs with cloud computing.

Langmead Ben B   Schatz Michael C MC   Lin Jimmy J   Pop Mihai M   Salzberg Steven L SL  

Genome biology 20091120 11

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  ...[more]

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