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

Genome Biology
Ben LangmeadSteven L Salzberg

Abstract

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 (http://bowtie.cbcb.umd.edu).

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Nov 30, 2012·Nucleic Acids Research·Sooyoung ChoSanghyuk Lee
Dec 12, 2012·Nucleic Acids Research·Jiyuan AnColleen C Nelson
Dec 4, 2012·Nucleic Acids Research·Wei-Chung ChengHsei-Wei Wang
Dec 22, 2012·Nucleic Acids Research·Chung-Chau HonNancy Guillen
Dec 22, 2012·Nucleic Acids Research·Shinpei KawaokaSusumu Katsuma
Jan 9, 2013·Nucleic Acids Research·Andrew Paul HutchinsDiego Miranda-Saavedra
Dec 21, 2012·Nucleic Acids Research·Yang LiJian Ma
Feb 22, 2012·Nucleic Acids Research·Aniruddha ChatterjeeIan M Morison
Mar 2, 2012·Nucleic Acids Research·Gong ZhangZoya Ignatova
Mar 30, 2012·Nucleic Acids Research·Martin C FrithKiyoshi Asai
Apr 17, 2012·Nucleic Acids Research·Prasanna Kumar JuvvunaEugene V Makeyev
Apr 19, 2012·Nucleic Acids Research·Sheroy MinocherhomjiAsli Silahtaroglu
Apr 13, 2012·Nucleic Acids Research·Chengyang WangX Shirley Liu
Apr 13, 2012·Nucleic Acids Research·Paraskevi SalpeaBruce H Howard
Apr 24, 2012·Nucleic Acids Research·Ismahen AmmarZoltán Ivics
May 11, 2012·Nucleic Acids Research·Robert M GivensMichael J Buck
May 15, 2012·Nucleic Acids Research·René BöttcherP J van der Zaag
May 10, 2012·Nucleic Acids Research·Rocco PiazzaCarlo Gambacorti-Passerini
May 16, 2012·Nucleic Acids Research·Michaël VyvermanPeter Dawyndt
Jun 19, 2012·Nucleic Acids Research·Chikako RaganDenis C Bauer
Jun 26, 2012·Nucleic Acids Research·Aurélien A SérandourGilles Salbert
Jun 26, 2012·Nucleic Acids Research·Andreas UntergasserSteven G Rozen
Jul 14, 2012·Nucleic Acids Research·Mohan Bolisetty, Karen Beemon
Aug 3, 2012·Nucleic Acids Research·Gilbert L HenrySean R Eddy
Aug 1, 2012·Nucleic Acids Research·Katharina M MichalikKlaus Förstemann
Sep 4, 2012·Nucleic Acids Research·Martin S Lindner, Bernhard Y Renard
Sep 27, 2012·Nucleic Acids Research·Pascal GellertShizuka Uchida
Jan 29, 2013·Nucleic Acids Research·Clayton K CollingsJohn N Anderson
Oct 16, 2012·Nucleic Acids Research·Víctor Barrera, Miguel A Peinado
Feb 15, 2013·Nucleic Acids Research·Richard Patryk Ngondo-MbongoPhilippe Carbon
Feb 15, 2013·Nucleic Acids Research·Danai FimereliTomasz Konopka
Mar 9, 2013·Nucleic Acids Research·Yuichi ShiraishiSatoru Miyano
Mar 6, 2013·Nucleic Acids Research·James E DiCarloGeorge M Church
Apr 6, 2013·Nucleic Acids Research·Yang LiaoWei Shi
Apr 6, 2013·Nucleic Acids Research·Hai-Son LeZiv Bar-Joseph
Apr 11, 2013·Nucleic Acids Research·Jie WuChaolin Zhang
May 2, 2013·Nucleic Acids Research·Harm NijveenBen Vosman
Apr 30, 2013·Nucleic Acids Research·Marco LodriniHedwig E Deubzer
Jul 23, 2013·Nucleic Acids Research·Kelly Patrick StantonYuval Kluger
Aug 13, 2013·Nucleic Acids Research·Christopher R CabanskiD Neil Hayes
Aug 9, 2013·Nucleic Acids Research·Masahiko ImashimizuMikhail Kashlev
Sep 17, 2013·Nucleic Acids Research·Yun ZhuWei Wang
Apr 18, 2013·Plant & Cell Physiology·Olga A PostnikovaLev G Nemchinov
Aug 15, 2012·Toxicological Sciences : an Official Journal of the Society of Toxicology·Joost van DelftJos Kleinjans
Jan 30, 2013·Toxicological Sciences : an Official Journal of the Society of Toxicology·Kai WangDavid J Galas
Jul 4, 2012·Molecular Plant-microbe Interactions : MPMI·Tiyakhon ChatnaparatSteven E Lindow
Aug 2, 2013·Molecular Plant-microbe Interactions : MPMI·Mario R de O BarsottiniAndre L B Ambrosio
Mar 2, 2012·Molecular Plant-microbe Interactions : MPMI·Sampurna SattarGary A Thompson
Jan 15, 2014·International Journal of Gynecological Cancer : Official Journal of the International Gynecological Cancer Society·Winnie S LiangBradley J Monk
Nov 23, 2012·Proceedings. Biological Sciences·Shuji Shigenobu, David L Stern
Dec 28, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Paul A HohenloheWilliam A Cresko
Jul 11, 2012·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Richard H BakerGerald S Wilkinson
Dec 4, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Irina EpsteinErin M Schuman
Nov 17, 2011·Genes & Development·Maria BergslandJonas Muhr
Dec 14, 2011·Genes & Development·Yevgenia L KhodorMichael Rosbash
Mar 7, 2012·Genes & Development·Subhashini SadasivamJames A DeCaprio
May 3, 2012·Genes & Development·Frédéric PontvianneCraig S Pikaard
Mar 3, 2010·Genes & Development·Michael SnyderMark Gerstein
May 3, 2012·Genes & Development·Jung-Shin LeeAli Shilatifard
Jun 21, 2012·Genes & Development·Darwin S Dichmann, Richard M Harland
Apr 24, 2010·Genes & Development·H Rosaria ChiangDavid P Bartel
Sep 14, 2012·Genes & Development·Jason DolesWilliam M Keyes
Sep 6, 2012·Genes & Development·Keun Pyo LeeLuis Lopez-Molina
Apr 18, 2013·Genes & Development·Alireza GhamariFrank G Grosveld
Mar 31, 2011·Genes & Development·Guillermo Pablo VicentMiguel Beato
Jan 14, 2010·Genome Research·John E PoolRasmus Nielsen
Jul 14, 2009·Genome Research·David WeeseKnut Reinert