Searching for SNPs with cloud computing

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...

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Detalles Bibliográficos
Autores principales: Langmead, Ben, Schatz, Michael C, Lin, Jimmy, Pop, Mihai, Salzberg, Steven L
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091327/
https://www.ncbi.nlm.nih.gov/pubmed/19930550
http://dx.doi.org/10.1186/gb-2009-10-11-r134
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author Langmead, Ben
Schatz, Michael C
Lin, Jimmy
Pop, Mihai
Salzberg, Steven L
author_facet Langmead, Ben
Schatz, Michael C
Lin, Jimmy
Pop, Mihai
Salzberg, Steven L
author_sort Langmead, Ben
collection PubMed
description 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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spelling pubmed-30913272011-05-10 Searching for SNPs with cloud computing Langmead, Ben Schatz, Michael C Lin, Jimmy Pop, Mihai Salzberg, Steven L Genome Biol Software 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/. BioMed Central 2009 2009-11-20 /pmc/articles/PMC3091327/ /pubmed/19930550 http://dx.doi.org/10.1186/gb-2009-10-11-r134 Text en Copyright ©2009 Langmead et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software
Langmead, Ben
Schatz, Michael C
Lin, Jimmy
Pop, Mihai
Salzberg, Steven L
Searching for SNPs with cloud computing
title Searching for SNPs with cloud computing
title_full Searching for SNPs with cloud computing
title_fullStr Searching for SNPs with cloud computing
title_full_unstemmed Searching for SNPs with cloud computing
title_short Searching for SNPs with cloud computing
title_sort searching for snps with cloud computing
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091327/
https://www.ncbi.nlm.nih.gov/pubmed/19930550
http://dx.doi.org/10.1186/gb-2009-10-11-r134
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