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

Ben Langmead; Cole Trapnell; Mihai Pop; Steven L. Salzberg · Genome biology · 2009

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Author / responsible party
Ben Langmead; Cole Trapnell; Mihai Pop; Steven L. Salzberg
Publisher
Genome biology
Year
2009
Language
English

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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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APA 7

Langmead, B, Trapnell, C, Pop, M, & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. https://doi.org/10.1186/gb-2009-10-3-r25

MLA

Langmead, Ben, et al. "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome." 2009. https://doi.org/10.1186/gb-2009-10-3-r25.

Chicago

Langmead, Ben, Cole Trapnell, Mihai Pop, and Steven L. Salzberg. 2009. "Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.". https://doi.org/10.1186/gb-2009-10-3-r25.

Harvard

Langmead, B. et al. 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome biology, available at: https://doi.org/10.1186/gb-2009-10-3-r25 [Accessed 8 Aug. 2026].

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Title
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Author / contributors
Ben Langmead; Cole Trapnell; Mihai Pop; Steven L. Salzberg
Publisher
Genome biology
Publication year
2009
Language
English

Subjects

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Biology; Human genetics; Human genome; Genome; Computational biology; Genetics; Genome Biology; Computational genomics; DNA; DNA sequencing; Evolutionary biology; Genomics
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