Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends prev...

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Detalles Bibliográficos
Autores principales: Langmead, Ben, Trapnell, Cole, 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/PMC2690996/
https://www.ncbi.nlm.nih.gov/pubmed/19261174
http://dx.doi.org/10.1186/gb-2009-10-3-r25
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author Langmead, Ben
Trapnell, Cole
Pop, Mihai
Salzberg, Steven L
author_facet Langmead, Ben
Trapnell, Cole
Pop, Mihai
Salzberg, Steven L
author_sort Langmead, Ben
collection PubMed
description Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source .
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spelling pubmed-26909962009-06-04 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Langmead, Ben Trapnell, Cole Pop, Mihai Salzberg, Steven L Genome Biol Software Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds. Bowtie is open source . BioMed Central 2009 2009-03-04 /pmc/articles/PMC2690996/ /pubmed/19261174 http://dx.doi.org/10.1186/gb-2009-10-3-r25 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
Trapnell, Cole
Pop, Mihai
Salzberg, Steven L
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title_full Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title_fullStr Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title_full_unstemmed Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title_short Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
title_sort ultrafast and memory-efficient alignment of short dna sequences to the human genome
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996/
https://www.ncbi.nlm.nih.gov/pubmed/19261174
http://dx.doi.org/10.1186/gb-2009-10-3-r25
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AT popmihai ultrafastandmemoryefficientalignmentofshortdnasequencestothehumangenome
AT salzbergstevenl ultrafastandmemoryefficientalignmentofshortdnasequencestothehumangenome

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