Searching for SNPs with cloud computing
Ben Langmead , Michael C Schatz , Jimmy Lin , Mihai Pop and Steven L Salzberg
Genome Biology 2009, 10:R134
doi:10.1186/gb-2009-10-11-r134
Published: 20 November 2009
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.sf.net/crossbow.
Ben Langmead , Michael C Schatz , Jimmy Lin , Mihai Pop and Steven L Salzberg
Genome Biology 2009, 10:R134
doi:10.1186/gb-2009-10-11-r134
Published: 20 November 2009
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.sf.net/crossbow.
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