Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.

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

Langmead B, Trapnell C, Pop M, Salzberg SL.

Source

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA. langmead@cs.umd.edu

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).

Comment in

Genome Biol. 2009;10(3):212.

PMID:: 19261174; [PubMed - indexed for MEDLINE]
PMCID: PMC2690996

Free PMC Article

Images from this publication.See all images (3) Free text

Publication Types, MeSH Terms, Grant Support

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Grant Support

LinkOut - more resources

Full Text Sources

Other Literature Sources

Supplemental Content

Related citations

Fast and accurate long-read alignment with Burrows-Wheeler transform. [Bioinformatics. 2010]
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li H, Durbin R. Bioinformatics. 2010 Mar 1; 26(5):589-95. Epub 2010 Jan 15.
Ψ-RA: a parallel sparse index for genomic read alignment. [BMC Genomics. 2011]
Ψ-RA: a parallel sparse index for genomic read alignment.
Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B. BMC Genomics. 2011; 12 Suppl 2:S7. Epub 2011 Jul 27.
SOAP2: an improved ultrafast tool for short read alignment. [Bioinformatics. 2009]
SOAP2: an improved ultrafast tool for short read alignment.
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. Bioinformatics. 2009 Aug 1; 25(15):1966-7. Epub 2009 Jun 3.
Fast and accurate short read alignment with Burrows-Wheeler transform. [Bioinformatics. 2009]
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R. Bioinformatics. 2009 Jul 15; 25(14):1754-60. Epub 2009 May 18.
Review Space-efficient whole genome comparisons with Burrows-Wheeler transforms. [J Comput Biol. 2005]
Review Space-efficient whole genome comparisons with Burrows-Wheeler transforms.
Lippert RA. J Comput Biol. 2005 May; 12(4):407-15.

See reviews... See all...

Cited by over 100 PubMed Central articles

Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology. [Front Genet. 2011]
Characterizing ncRNAs in Human Pathogenic Protists Using High-Throughput Sequencing Technology.
Collins LJ. Front Genet. 2011; 2:96. Epub 2011 Dec 27.
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing. [Front Genet. 2011]
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing.
Liu W, Zhao Y, Cui P, Lin Q, Ding F, Xin C, Tan X, Song S, Yu J, Hu S. Front Genet. 2011; 2:93. Epub 2011 Dec 26.
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data. [Front Genet. 2011]
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data.
Huang S, Zhang J, Li R, Zhang W, He Z, Lam TW, Peng Z, Yiu SM. Front Genet. 2011; 2:46. Epub 2011 Jul 7.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Ultrafast and memory-efficient alignment of short DNA sequences to the human gen...
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol. 2009 ;10(3):R25. Epub 2009 Mar 4 .

PubMed
Skin lightening preparations and the hydroquinone controversy.
Skin lightening preparations and the hydroquinone controversy.
Dermatol Ther. 2007 Sep-Oct ;20(5):308-13.

PubMed
Porcine induced pluripotent stem cells produce chimeric offspring.
Porcine induced pluripotent stem cells produce chimeric offspring.
Stem Cells Dev. 2010 Aug ;19(8):1211-20.

PubMed
Studies on transformation of Escherichia coli with plasmids.
Studies on transformation of Escherichia coli with plasmids.
J Mol Biol. 1983 Jun 5 ;166(4):557-80.

PubMed
Zooflagellate phylogeny and classification.
Zooflagellate phylogeny and classification.
Tsitologiia. 1995 ;37(11):1010-29.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Display Settings:

Send to: