UNIT 15.3 Genotyping in the Cloud with Crossbow
Published Online: 1 SEP 2012
Copyright © 2012 by John Wiley & Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Gurtowski, J., Schatz, M. C. and Langmead, B. 2012. Genotyping in the Cloud with Crossbow. Current Protocols in Bioinformatics. 39:15.3:15.3.1–15.3.15.
- Published Online: 1 SEP 2012
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.
- short reads;
- read alignment;
- SNP calling;
- cloud computing;
- software package