Cited by 12,063Genomics and Phylogenetic StudiesAlgorithms and Data CompressionFractal and DNA sequence analysis

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Fast and accurate long-read alignment with Burrows-Wheeler transform.

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Li, Heng, Durbin, Richard·2010·Bioinformatics

DOI 10.1093/bioinformatics/btp698PMC PMC2828108

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Abstract

Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk

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Fig. 1. Prefix trie and prefix DAWG of string ‘GOOGOL’. (A) Prefix trie. Symbol ‘∧’ marks the start of a string. The two numbers in a node gives the SA interval of the node. (B) Prefix DAWG constructed by collapsing nodes with the identical SA interval. For example, in the prefix trie, three nodes has SA interval [4, 4]. Their parents have interval [1, 2], [1, 2] and [1, 1], respectively. In the prefix DAWG, the [4, 4] node thus has parents [1, 2] and [1, 1]. Node [4, 4] represents three strings ‘OG’, ‘OGO’ and ‘OGOL’ with the first two strings being the prefix of ‘OGOL’. (A) is modified from Figure 1 in Li and Durbin (2009).CC BY-NC · PubMed Central

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Self-citation
Fast and accurate short read alignment with Burrows-Wheeler transform
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
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<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480 · cited 1×
“…and PatternHunter (Ma et al ., 2002), greatly speeding up matching capillary sequencing technologies arrived that generated millions of short (<100bp) reads, a variety of new algorithms were developed which were 10–1000 times faster, including SOAP (Li,R. et al 2008), MAQ (Li,H. et al ., 2009).”
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Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459 · cited 1×
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SOAP: Short oligonucleotide alignment program
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“Memory required for each query is roughly proportional to <4GB; on one query sequence with 1 million base pairs (Mbp), peak memory is”
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Real-time DNA sequencing from single polymerase molecules.
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Burrows, 1994, A block-sorting lossless data compression algorithm

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“…including whole genome alignment (Delcher et al. 1999, Lin and Hsu 2020), read mapping (Langmead et al. 2009, Li and Durbin 2009), read alignment (Li and Durbin 2010), identical by descent (IBD) segment detection (Naseri et al. 2019, Freyman et al. 2021), metagenomic or taxonomic classification…”

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: 2010-01-15
Volume: 26
Issue: 5
Pages: 589-595
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btp698
PMC: PMC2828108
OpenAlex: W4247053599
Cited by: 12,063
References: 24
Citations by year: 2026: 639 · 2025: 972 · 2024: 1129 · 2023: 1067 · 2022: 1203 · 2021: 1245 · 2020: 1176 · 2019: 941 · 2018: 826 · 2017: 747 · 2016: 574 · 2015: 498 · 2014: 419 · 2013: 301 · 2012: 203
FWCI: 80.44
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/2.0/uk/ (vor, 2452 d)
Locations: Bioinformatics (publishedVersion, cc-by-nc)
Funders: Wellcome Trust (077192/Z/05/Z)
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: long-read alignment, Burrows-Wheeler transform, Smith-Waterman alignment, sequence alignment, reference genome, blat, alignment speed, alignment accuracy, human genome

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Fast and accurate long-read alignment with Burrows-Wheeler transform.

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