Searching for SNPs with cloud computing.

Genome Biology
Ben LangmeadSteven L Salzberg

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/.

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Methods Mentioned

BETA
genotyping
RNA-seq
ChIP-seq

Software Mentioned

Illumina
KeyFieldBasedPartitioner
CloudBurst
SOAPsnp
Hadoop Distributed Filesystem ( HDFS )
BeadChip
Bowtie
BlueGene
MapReduce
SOAP aligner

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