Open Access

Nature Methods, volume 9, issue 4, pages 357-359

Fast gapped-read alignment with Bowtie 2

Langmead Ben ^{1, 2}

Salzberg Steven L. ^{1, 2, 3}

Hide authors affiliations Show authors affiliations: 3 affiliations

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, USA |

Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA |

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA |

Publication type: Journal Article

Publication date: 2012-03-04

Springer Nature

Journal: Nature Methods

Quartile SCImago

Quartile WOS

Impact factor: 48

ISSN: 15487091, 15487105

DOI: 10.1038/nmeth.1923

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PubMed ID: 22388286

Biochemistry

Molecular Biology

Cell Biology

Biotechnology

Abstract

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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Nature	Nature, 300, 0.79% Nature 300 publications, 0.79%
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Science	Science, 209, 0.55% Science 209 publications, 0.55%
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Citations by publishers

	1000 2000 3000 4000 5000 6000 7000 8000 9000
Springer Nature	Springer Nature, 8326, 21.98% Springer Nature 8326 publications, 21.98%
Elsevier	Elsevier, 5319, 14.04% Elsevier 5319 publications, 14.04%
Wiley	Wiley, 2327, 6.14% Wiley 2327 publications, 6.14%
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Genetics Society of America	Genetics Society of America, 341, 0.9% Genetics Society of America 341 publications, 0.9%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 268, 0.71% Proceedings of the National Academy of Sciences (PNAS) 268 publications, 0.71%
PeerJ	PeerJ, 222, 0.59% PeerJ 222 publications, 0.59%
Microbiology Society	Microbiology Society, 196, 0.52% Microbiology Society 196 publications, 0.52%
American Chemical Society (ACS)	American Chemical Society (ACS), 162, 0.43% American Chemical Society (ACS) 162 publications, 0.43%
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EMBO press	EMBO press, 135, 0.36% EMBO press 135 publications, 0.36%
American Society of Plant Biologists	American Society of Plant Biologists, 121, 0.32% American Society of Plant Biologists 121 publications, 0.32%
The Royal Society	The Royal Society, 94, 0.25% The Royal Society 94 publications, 0.25%
Wolters Kluwer Health	Wolters Kluwer Health, 84, 0.22% Wolters Kluwer Health 84 publications, 0.22%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 81, 0.21% American Society for Biochemistry and Molecular Biology 81 publications, 0.21%
American Society for Clinical Investigation	American Society for Clinical Investigation, 76, 0.2% American Society for Clinical Investigation 76 publications, 0.2%
Mary Ann Liebert	Mary Ann Liebert, 76, 0.2% Mary Ann Liebert 76 publications, 0.2%
Hindawi Limited	Hindawi Limited, 76, 0.2% Hindawi Limited 76 publications, 0.2%
	1000 2000 3000 4000 5000 6000 7000 8000 9000

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GOST |

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GOST Copy

Langmead B. et al. Fast gapped-read alignment with Bowtie 2 // Nature Methods. 2012. Vol. 9. No. 4. pp. 357-359.

GOST all authors (up to 50) Copy

Langmead B., Salzberg S. L. Fast gapped-read alignment with Bowtie 2 // Nature Methods. 2012. Vol. 9. No. 4. pp. 357-359.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1038/nmeth.1923

UR - https://doi.org/10.1038%2Fnmeth.1923

TI - Fast gapped-read alignment with Bowtie 2

T2 - Nature Methods

AU - Langmead, Ben

AU - Salzberg, Steven L.

PY - 2012

DA - 2012/03/04 00:00:00

PB - Springer Nature

SP - 357-359

IS - 4

VL - 9

PMID - 22388286

SN - 1548-7091

SN - 1548-7105

ER -

BibTex |

Cite this

BibTex Copy

@article{2012_Langmead,

author = {Ben Langmead and Steven L. Salzberg},

title = {Fast gapped-read alignment with Bowtie 2},

journal = {Nature Methods},

year = {2012},

volume = {9},

publisher = {Springer Nature},

month = {mar},

url = {https://doi.org/10.1038%2Fnmeth.1923},

number = {4},

pages = {357--359},

doi = {10.1038/nmeth.1923}

}

MLA

Cite this

MLA Copy

Langmead, Ben, et al. “Fast gapped-read alignment with Bowtie 2.” Nature Methods, vol. 9, no. 4, Mar. 2012, pp. 357-359. https://doi.org/10.1038%2Fnmeth.1923.

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Springer Nature

Journal

Nature Methods

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Quartile WOS

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15487091 (Print)
15487105 (Electronic)