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Fast and accurate short read alignment with Burrows-Wheeler transform
Open accessAbstract
MOTIVATION: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. RESULTS: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. AVAILABILITY: http://maq.sourceforge.net.
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“For example, Martiniano et al. [9] find that the more relaxed parameters -n 0.02 -l 1024 -o 2 work best for BWA aln [10]”
From <tt>SAFARI</tt> : pangenome alignment of ancient DNA using purine/pyrimidine encodings (2025) · cites this paper as [10]
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“Allelic imbalance is commonly observed in a tissue-specific manner (51, 52).”
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Metadata
- Authors
- Li, H., & Durbin, R.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Durbin, Richard
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-18
- Volume
- 25
- Issue
- 14
- Pages
- 1754-1760
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC2705234
- OpenAlex
- W2103441770
- Cited by
- 58,607
- References
- 32
- Citations by year
- 2026: 3541 · 2025: 4985 · 2024: 5800 · 2023: 5335 · 2022: 5575 · 2021: 5916 · 2020: 5161 · 2019: 4192 · 2018: 3819 · 2017: 3299 · 2016: 2900 · 2015: 2520 · 2014: 2193 · 2013: 1586 · 2012: 1007
- FWCI
- 233.42
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (077192/Z/05/Z)
- Broad Institute
- 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
- short-read alignment, Burrows-Wheeler transform, BWA, gapped alignment, indels, backward search, variant calling, resequencing, human genome, DNA sequencing
- MeSH terms
- Algorithms, Software, Sequence Alignment, Sequence Analysis, DNA, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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