The DOI matches its Crossref record; 22 of the 24 references it cites were found in a registry or an index.
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Open accessAbstract
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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“Software confirmed to be working for this approach include (but are not limited to) Bowtie2 11, BWA 12, HISAT2 13, STAR 14 or any tool wrapping one of these aligners.”
From SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes (2016) · cites this paper as [12]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Mapping reads to specific genes is relatively straightforward with the bioinformatics tools available today [10-13], but using these tools to distinguish between reads derived from alternative alleles of the same gene remains challenging [9].”
From Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome (2013) · cites this paper as [11]
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Citations
Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · cited 1×
“Cambridge, CB10 1SA, UK such as FASTA (Pearson and Lipman, 1988) and BLAST (Altschul MegaBLAST (Morgulis et al ., 2008; Zhang et al ., 2000), SSAHA2 (Ning et al ., 2001), BLAT (Kent, 2002) and PatternHunter (Ma et al ., 2002), greatly speeding up matching capillary sequencing technologies arrived…”
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Self-citationFast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Self-citationUltrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227 · cited 4×
“Cambridge, CB10 1SA, UK such as FASTA (Pearson and Lipman, 1988) and BLAST (Altschul MegaBLAST (Morgulis et al ., 2008; Zhang et al ., 2000), SSAHA2 (Ning et al ., 2001), BLAT (Kent, 2002) and PatternHunter (Ma et al ., 2002), greatly speeding up matching capillary sequencing technologies arrived…”
Influential<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).”
A Greedy Algorithm for Aligning DNA Sequences
Zhang, Z., Schwartz, S., Wagner, L., & Miller, W. (2000) · Journal of Computational Biology · doi:10.1089/10665270050081478 · Cited by 5,459 · cited 1×
“…SSAHA2 (Ning et al ., 2001), BLAT (Kent, 2002) 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: Short oligonucleotide alignment program
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638 · cited 1×
“Memory required for each query is roughly proportional to <4GB; on one query sequence with 1 million base pairs (Mbp), peak memory is”
Self-citationReal-time DNA sequencing from single polymerase molecules.
Korlach, J., Bjornson, K., Chaudhuri, B., Cicero, R., Flusberg, B., Gray, J., Holden, D., Saxena, R., Wegener, J., & Turner, S. (2010) · Methods in Enzymology · doi:10.1016/s0076-6879(10)72001-2 · Cited by 1,847
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- Burrows, 1994, A block-sorting lossless data compression algorithm
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Items 1,201–1,225 of 1,225
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“17,18 The GATK Genotype tool was employed to call variants, which were then stored as a VCF file.”
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“…on DNBSEQ-T7 platform, as described earlier [22 ], ultimately generating FASTQ files with read lengths of 100–200 bp. Quality control was conducted with fastp, and then the clean data were mapped to the human reference genome (UCSC hg19) with Burrow-Wheeler Aligner (BWA, version 0.7.17) [ 23 ].”
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“7.17 ‐ r1188) (Li and Durbin 2010).”
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“0) using BWA-MEM (50) and pre-processed following standard GATK protocols (51).”
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“7.17) [ 40 ].”
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Pan, C., Ma, L., Wang, L.-L., Zhang, Z.-B., Wang, A., Bai, F.-T., Cai, Y., Ma, Y., Wang, Y.-C., Liu, G.-L., et al. (2025) · bioRxiv · doi:10.1101/2025.07.28.667120
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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
- 2010-01-15
- Volume
- 26
- Issue
- 5
- Pages
- 589-595
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- 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
- 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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