Open AccessGenotyping in the Cloud with Crossbow
Author(s) -
Gurtowski James,
Schatz Michael C.,
Langmead Ben
Publication year - 2012
Publication title -
current protocols in bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.535
H-Index - 57
eISSN - 1934-340X
pISSN - 1934-3396
DOI - 10.1002/0471250953.bi1503s39
Subject(s) - cloud computing , computer science , operating system , scalability , software , cluster (spacecraft) , computer cluster , database
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. Curr. Protoc. Bioinform . 39:15.3.1‐15.3.15. © 2012 by John Wiley & Sons, Inc.