Searching for SNPs with cloud computing

被引：323

作者：

Langmead, Ben ^{[1
,2
]}

Schatz, Michael C. ^{[2
]}

Lin, Jimmy ^{[3
]}

Pop, Mihai ^{[2
]}

Salzberg, Steven L. ^{[2
]}

机构：

[1] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Biostat, Baltimore, MD 21205 USA

[2] Univ Maryland, Ctr Bioinformat & Computat Biol, College Pk, MD 20742 USA

[3] Univ Maryland, Coll Informat Studies, The iSchool, College Pk, MD 20742 USA

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 11期

关键词：

HUMAN GENOME; SHORT-READ; RNA-SEQ; SEQUENCE; ALIGNMENT;

D O I：

10.1186/gb-2009-10-11-r134

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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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