title: Genotyping in the cloud with Crossbow.
abstract: Crossbow is a scalable, portable, and automatic cloud computing tool for identifying SNPs from high-coverage, short-read resequencing data. It is built on Apache Hadoop, an implementation of the MapReduce software framework. Hadoop allows Crossbow to distribute read alignment and SNP calling subtasks over a cluster of commodity computers. Two robust tools, Bowtie and SOAPsnp, implement the fundamental alignment and variant calling operations respectively, and have demonstrated capabilities within Crossbow of analyzing approximately one billion short reads per hour on a commodity Hadoop cluster with 320 cores. Through protocol examples, this unit will demonstrate the use of Crossbow for identifying variations in three different operating modes: on a Hadoop cluster, on a single computer, and on the Amazon Elastic MapReduce cloud computing service.
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
authors.forename: James
authors.initials: J
authors.lastname: Gurtowski
authors.affiliation: Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Schatz
authors.affiliation: Department of Computer Science, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.
authors.forename: Ben
authors.initials: B
authors.lastname: Langmead
mesh_terms: D000465:Algorithms; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D012984:Software