Searching for SNPs with cloud computing

Langmead, B., Schatz, M. C., Lin, J., Pop, M., Salzberg, S. L. (2009) Searching for SNPs with cloud computing. Genome Biology, 10 (11). ISSN 14747596 (ISSN)

[thumbnail of Paper]
PDF (Paper)
Schatz Genome Biology 2009b.pdf - Published Version

Download (612kB) | Preview
DOI: 10.1186/gb-2009-10-11-r134


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© 2009 Langmead et al; licensee BioMed Central Ltd.

Item Type: Paper
Additional Information:
Uncontrolled Keywords: accuracy article chromosome 22 computer program diploidy gene frequency gene sequence genotype haploidy heterozygosity homozygosity human human chromosome human genome sensitivity and specificity single nucleotide polymorphism X chromosome algorithm allele biological model biology chromosome computer computer simulation DNA sequence genetics heterozygote methodology ultrastructure Algorithms Alleles Chromosomes Chromosomes, Human, Pair 22 Chromosomes, Human, X Computational Biology Computers Humans Models, Genetic Polymorphism, Single Nucleotide Sequence Analysis DNA Software
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
bioinformatics > genomics and proteomics > alignment > sequence alignment
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > computers > computer software
Investigative techniques and equipment > interface method
CSHL Authors:
Communities: CSHL labs > Schatz lab
Depositing User: CSHL Librarian
Date: 2009
Date Deposited: 16 Mar 2012 15:27
Last Modified: 15 Mar 2013 19:14
PMCID: PMC3091327
Related URLs:

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving