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Searching for SNPs with cloud computing
- Langmead, Ben, Schatz, Michael C, Lin, Jimmy, Pop, Mihai, Salzberg, Steven L
- Genome biology 2009 v.10 no.11 pp. 2284
- computer software, computers, genome, humans, sequence analysis, single nucleotide polymorphism
- 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/ .