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Genome Biol. 2009;10(3):R25. doi: 10.1186/gb-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).

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The need for speed. [Genome Biol. 2009]
The need for speed.Flicek P. Genome Biol. 2009; 10(3):212. Epub 2009 Mar 27.

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

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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. doi: 10.1186/gb-2009-10-3-r25. Epub 2009 Mar 4 .

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