Cited by 21,849Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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

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Langmead, Ben, Trapnell, Cole, Pop, Mihai, Salzberg, Steven L·2009·Genome Biology

DOI 10.1186/gb-2009-10-3-r25PMC PMC2690996

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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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Figure 1 Burrows-Wheeler transform. (a) The Burrows-Wheeler matrix and transformation for 'acaacg'. (b) Steps taken by EXACTMATCH to identify the range of rows, and thus the set of reference suffixes, prefixed by 'aac'. (c) UNPERMUTE repeatedly applies the last first (LF) mapping to recover the original text (in red on the top line) from the Burrows-Wheeler transform (in black in the rightmost column).CC BY · PubMed Central

Figure 2 Exact matching versus inexact alignment. Illustration of how EXACTMATCH (top) and Bowtie's aligner (bottom) proceed when there is no exact match for query 'ggta' but there is a one-mismatch alignment when 'a' is replaced by 'g'. Boxed pairs of numbers denote ranges of matrix rows beginning with the suffix observed up to that point. A red X marks where the algorithm encounters an empty range and either aborts (as in EXACTMATCH) or backtracks (as in the inexact algorithm). A green check marks where the algorithm finds a nonempty range delimiting one or more occurrences of a reportable alignment for the query.CC BY · PubMed Central

Figure 3 The three phases of the Bowtie algorithm for the Maq-like policy. A three-phase approach finds alignments for two-mismatch cases 1 to 4 while minimizing backtracking. Phase 1 uses the mirror index and invokes the aligner to find alignments for cases 1 and 2. Phases 2 and 3 cooperate to find alignments for case 3: Phase 2 finds partial alignments with mismatches only in the hi-half, and phase 3 attempts to extend those partial alignments into full alignments. Finally, phase 3 invokes the aligner to find alignments for case 4.CC BY · PubMed Central

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Authors: Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L.
Affiliations: University of Maryland, College Park (US)
Corresponding author: Langmead, Ben
ORCID: Langmead, Ben
Trapnell, Cole
Pop, Mihai
Salzberg, Steven L
Venue: Genome Biology
Publisher: Springer Science and Business Media LLC
Published: 2009-03-04
Volume: 10
Issue: 3
Pages: R25-R25
ISSN: 1465-6906 (ISSN-L)
1474-760X
DOI: 10.1186/gb-2009-10-3-r25
PMC: PMC2690996
OpenAlex: W2124985265
Cited by: 21,849
References: 29
Citations by year: 2026: 620 · 2025: 981 · 2024: 1140 · 2023: 1226 · 2022: 1405 · 2021: 1665 · 2020: 1652 · 2019: 1726 · 2018: 1653 · 2017: 1702 · 2016: 1538 · 2015: 1620 · 2014: 1565 · 2013: 1325 · 2012: 1029
FWCI: 267.58
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/2.0/ (tdm)
creativecommons.org/licenses/by/2.0/ (vor)
Locations: Genome biology (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
University Libraries (University of Maryland) (submittedVersion)
Digital Repository at the University of Maryland (University of Maryland College Park)
Funders: National Institutes of Health
National Human Genome Research Institute (R01HG004885)
National Institute of General Medical Sciences (R01GM083873)
U.S. National Library of Medicine (R01LM006845)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Mathematics › Theoretical Computer Science › Algorithms and Data Compression
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords: Bowtie, human genome, memory-efficient alignment, parallel alignment, next-generation sequencing reads
MeSH terms: Algorithms, Base Sequence, Humans, Genome, Human, Sequence Alignment

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

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