Cited by 58,607Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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Fast and accurate short read alignment with Burrows-Wheeler transform

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Li, Heng, Durbin, Richard·2009·Bioinformatics

DOI 10.1093/bioinformatics/btp324PMC PMC2705234

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Abstract

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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The Sequence Alignment/Map format and SAMtools
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Self-citation
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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Authors: Li, H., & Durbin, R.
Affiliations: Wellcome Sanger Institute (GB)
Corresponding author: Durbin, Richard
ORCID: Li, Heng
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
DOI: 10.1093/bioinformatics/btp324
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: cc-by-nc
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2694 d)
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

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Fast and accurate short read alignment with Burrows-Wheeler transform

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