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)
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Abstract
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/.© 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: | |
| URI: | https://repository.cshl.edu/id/eprint/25361 |
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