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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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![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).](/paper-figures/1df6af5164514755b0a07be87022bd5e/fast-and-accurate-long-read-alignment-with-burrows-wheeler-transform-figure-1.jpg)
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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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Cites
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The Sequence Alignment/Map format and SAMtools
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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.
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“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×
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Self-citationReal-time DNA sequencing from single polymerase molecules.
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- Burrows, 1994, A block-sorting lossless data compression algorithm
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“…nload. soe. ucsc. edu/ golde nPath/ mm10/ bigZi ps/ latest/ mm10. fa. gz) or the FVB reference genome for the cortex samples (https:// ftp. ensem bl. org / pub/ relea se-108/ fasta/ mus_ muscu lus_ fvbnj/ dna/ Mus_ muscu lus_ fvbnj. FVB_ NJ_ v1. dna . tople vel. fa. gz ) using BWA-MEM [20, 21].”
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“Version 2.7.11b) [23–27].”
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InfluentialSalaria, S., Boatwright, L., Vandemark, G., & Thavarajah, D. (2025) · The Plant Genome · doi:10.1002/tpg2.70152
Lv, K., Chen, Y., Zhou, J.-C., Ji, F.-Y., & Hu, W.-X. (2025) · BMC Biotechnology · doi:10.1186/s12896-025-01053-6
“The clean data were aligned to the human reference genome (version GRCh38) using BWA [26], and the alignment results were further processed with Picard to remove duplicates, ultimately generating the alignment result BAM files.”
Cioni, L., Guerrini, V., & Rosone, G. (2025) · Theoretical Computer Science · doi:10.1016/j.tcs.2025.115626
Evaluating the Utility of Fresh Tissue in Molecular Diagnostics of Colorectal Cancer
Kałużewski, T., Wcisło, S., Sałacińska, K., Kępczyński, Ł., Kubiak, I., Grabiec, M., Kalinka, E., Kałużewski, B., & Gach, A. (2025) · Cancers · doi:10.3390/cancers17223709
“Prior to variant calling, sequencing reads were aligned to the hg19 reference genome using BWA (v.0.7.17) [24], and converted to BAM format using SAMtools (v1.”
InfluentialJang, W., Lee, S. H., Kim, W. J., Yang, S., & Moon, B. C. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262211189
“7.17 [26] and samtools v1.”
InfluentialGenetic structure of Shandong taurine cattle in Han Dynasty
Bai, T., He, H., Shen, Q., Xu, Y., Tao, L., Zhu, K., Wang, R., Zheng, J., Liu, Y., Mao, X., et al. (2025) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2025.105401
Genomic analyses identify distinct patterns of selection in game fowl and Nami chicken
Gong, W., Ning, T., Ran, J.-S., Li, D.-Y., Huang, W., Yu, J., Yang, Y., Zhu, Y., Dong, C., Zhou, M., et al. (2025) · Poultry Science · doi:10.1016/j.psj.2025.106095
Kumagai, N., Kuroda, M., Hanai, T., Fujita, M., Hino, T., Yorimoto, S., Manta, S., Nakagawa, S., Yokoyama, M., Tajima, L., et al. (2025) · PLoS Genetics · doi:10.1371/journal.pgen.1011944
“After trimming, they were mapped to transcriptome data using BWA mem [95–97].”
Biological characteristics and genomic study of two Vibrio alginolyticus phages.
Zhang, Y., Luo, Y., Liu, C., Liu, G.-F., Jiang, L.-L., Wang, X., Li, M.-Y., Zhang, H.-S., Lai, X.-F., & Jiang, J.-Z. (2025) · Virology · doi:10.1016/j.virol.2025.110744
Burghardt, L., Sydow, P., Sutherland, J., Epstein, B., & Tiffin, P. (2025) · bioRxiv · doi:10.1101/2025.06.16.659998
Teng, X., Zhao, J., Shen, J., Yao, J., Tang, L., Xu, J., Chen, Y., & Wang, L.-Q. (2025) · Clinical and Experimental Obstetrics & Gynecology · doi:10.31083/ceog41691
“7.17, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK) [11].”
InfluentialSquire: A General-Purpose Accelerator to Exploit Fine-Grain Parallelism on Dependency-Bound Kernels
Langarita, R., Alastruey-Benedé, J., Ibáñez-Marín, P., Marco-Sola, S., Moretó, M., & Armejach, A. (2025) · International Conference on Parallel Architectures and Compilation Techniques · doi:10.1109/pact65351.2025.00035
A novel VPS13A mutation in an Iranian family with Chorea-Acanthocytosis
Salmanian, M., Mohammadian, F., & Alizadeh, F. (2025) · Neurogenetics · doi:10.1007/s10048-025-00855-2
“The Burrows-Wheeler aligner aligned the raw data to the human reference genome (hg19) [12].”
ScalableAligner: a fast NGS mapping tool for shared-memory system
Tang, D., Liang, J., Zhang, P., & Deng, Q.-W. (2025) · CCF Transactions on High Performance Computing · doi:10.1007/s42514-025-00244-z
“…and Man-zini 2005) are more widely used, such as Bowtie (Lang-mead et al. 2009)/Bowtie2 (Langmead and Salzberg 2012), BWA-MEM (Li 1303), BWA-SW (Li and Durbin 2010), BWA-MEM2 (Md et al. 2019), Subread (Liao et al. 2013), HISAT (Kim et al. 2015)/HISAT2 (Kim et al. 2019), etc., demonstrating…”
Ho, C.-H., Lu, W.-T., Wang, W.-K., Lin, C.-Y., Kuo, C.-H., & Chiou, L. (2025) · Biomedical Circuits and Systems Conference · doi:10.1109/biocas67066.2025.00022
“In this study, we compare the IMS-enhanced pipeline with a conventional workflow, including Burrows-Wheeler Aligner (BWA) [8] and the Genome Analysis Toolkit (GATK) [9], in terms of runtime, variant calling accuracy, and the capability to retain reads near short variant sites.”
Walsh, A. M., Roycroft, E., Hinchion, K., Basdeo, S., Sheedy, F. J., Crispie, F., Cotter, P., McLaughlin, A., Keane, J., Fitzgibbon, M., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01549-y
“7.18) [30] with the flag ‘-x intractg’.”
InfluentialMussa, B. M., Srivastava, A., Rajan, R., Venkatachalam, T., Al-Habshi, A., Abdelgadir, E., Bashier, A. M., Alawadi, F., Hafidh, K., Hamoudi, R., et al. (2025) · European journal of medical research · doi:10.1186/s40001-025-03105-1 · Cited by 1
Shaw, P. L., Slippers, B., Wingfield, B., Laurent, B., Penaud, B., Wingfield, M., Crous, P. W., Bihon, W., & Duong, T. A. (2025) · G3 · doi:10.1093/g3journal/jkaf239
“7.17-r1188 (Li and Durbin 2010).”
InfluentialBalimponya, E. G., Dwiyanti, M. S., Yamamori, K., Sakaguchi, S., Kanaoka, Y., Koide, Y., & Kishima, Y. (2025) · Plant Methods · doi:10.1186/s13007-025-01437-x
“Advancement in bioinformatics mapping tools including BWA-MEM2 [22, 23], Bowtie2 [24], SOAP2 [25], MapReads, SOCS [26], CLC genomic workbench (QIAGEN, Aarhus, Denmark), Novoalign (http:// novoc raft. com/) and BWA-SW [22] has also widened the choosing options in variant detection.”
Bulteau, S., Braud, M., Petrier, M., Castain, L., Anani, H., Peltier, C., Mobuchon, L., Bouras, M., Flattres, D., Poschmann, J., et al. (2025) · Journal of Medical Virology · doi:10.1002/jmv.70612
“Reads were trimmed using Cutadapt (vs 4.5) [29] and aligned to the human reference genome (hg38) by BWA ‐ MEM2 (2.2.1) [30].”
InfluentialChildren with Genetically Confirmed Hereditary Spastic Paraplegia: A Single-Center Experience
Besen, S., Özkale, Y., Özkale, M., Bozdoğan, S., Alkan, Ö., Ceylaner, S., & Erol, I. (2025) · Children · doi:10.3390/children12101332
“Alignment to (GRCh38) was performed using BWA-MEM 0.7.17 [8].”
InfluentialYan, K., Wang, J.-J., Tang, S., Yu, Z., & Li, J.-T. (2025) · Marine Biotechnology · doi:10.1007/s10126-025-10524-y
“R (Li and Durbin 2010).”
Understanding Callus Types in Maize by Genetic Mapping and Transcriptional Profiling
Lin, G.-F., Liu, Y., Tamang, T., Qin, Y., Zhao, M., Zheng, J., Wang, G.-Y., Wei, H.-R., Park, S., Cho, M.-J., et al. (2025) · Plants · doi:10.3390/plants14203168
“Reads were aligned to the B73 reference genome (B73Ref4) [54] with BWA [55].”
Ertürk, R. A., Emül, A. A., Darendeli-Kiraz, B. N., Sarı, F. Z., Ergün, M. A., & Baysan, M. S. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1013552
Kimmitt, A. A., Pegan, T. M., Wacker, K. S., Jones, A. W., & Winger, B. M. (2025) · Evolutionary Applications · doi:10.1111/eva.70163 · Cited by 1
“We aligned samples from each species in our dataset to a closely related species with an available chromosome-level reference genome (Table S2; Toews et al. 2016; Manthey et al. 2021; Friis et al. 2022) using bwa mem (Li and Durbin 2010) and Samtools (Li et al. 2009).”
Weak sperm differentiation in Darwin’s finches
Lifjeld, J., Garcia-del-Rey, E., Grønstøl, G., Valle, C. A., & Leder, E. (2025) · Biological Journal of the Linnean Society · doi:10.1093/biolinnean/blaf103
Shan, S., Qing, Y., Chen, S.-M., Liao, Y., Zhao, D., & Jiang, L.-C. (2025) · Data in Brief · doi:10.1016/j.dib.2025.112213
“The sequence assembled by NOVOPlasty was used as a reference for mapping using BWA-MEM [ 15 ].”
Liu, L., Huang, S. H., Jiang, F., Liang, G.-Q., Zhu, X., Zhu, H., & Tian, W. (2025) · Human Reproduction · doi:10.1093/humrep/deaf186 · Cited by 1
CTCF Mediates the Cis-Regulatory Hubs in Mouse Hearts
Lee, C. J. M., Mangnier, L., Padilla, C. C., Lee, D. P., Tan, W. L. W., Zheng, W. H., Gan, L. H., Chen, C. K., Lim, Y. P., Wang, R. M. Q., et al. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26199834
“7.19 [38].”
InfluentialSinkov, V. V., Ogarkov, O., Zhdanova, S., & Savilov, E. (2025) · Acta Biomedica Scientia · doi:10.29413/abs.2025-10.4.24
Jiang, X., Shi, L., Zhao, M., Chen, C., Tang, T., Ji, S., Lv, B., Jia, L., Duan, S., Ma, J.-Y., et al. (2025) · Frontiers in Genetics · doi:10.3389/fgene.2025.1643229
Alolod, G. A. L., Guzman, J. P. M. D., Matsumoto, S., Koiwai, K., Kondo, H., & Hırono, I. (2025) · Fisheries Science · doi:10.1007/s12562-025-01919-w
Simo, J., Janer, A., Antonicka, H., Macaron, G., Mégarbané, A., Massie, R., O'Ferrall, E., Karamchandani, J., Brais, B., Meijer, I., et al. (2025) · medRxiv · doi:10.1101/2025.09.17.25335877
“Paired-end, short-read WGS was performed on the NovaSeq6000 system (Illumina), reaching an average depth of coverage equal to 30X. Raw FASTQ read data generated from WGS were aligned to GRCh37 using the Burrows-Wheeler Aligner (BWA) 24 .”
Bonilla, B., Patty, B. J., Sambare, S., Dekker, J., Fazzio, T., & Hainer, S. J. (2025) · bioRxiv · doi:10.1101/2025.09.16.676562
“Raw fastq files for each replicate were aligned to the mm10 genome using BWA (H. Li and Durbin 2009, 2010) and the resulting sam files were downsampled to the smallest for each replicate using SAMtools (Danecek et al. 2021).”
SARS-CoV-2 infection dynamics in a MHCI-mismatched lung transplant recipient
Fuchs, J., Karl, V., Hettich, I., Alvarado, J., Eckert, D., Jaki, L., Kohl, A.-K., Kremser, A., Maks, A., Terschluse, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-63681-y
“The de-multiplexed raw reads were subjected to a custom Galaxy pipeline, which is based on SARS-CoV-2 analysis pipelines on usegalaxy.eu 52 The raw reads were pre-processed with fastp 53 and mapped to the SARS-CoV-2 Wuhan-Hu-1 reference genome (Genbank: NC_045512) using BWA-MEM 54 .”
Yang, T., Yang, R., Liu, Y., Feng, M., Li, Y.-Y., Zhang, H.-T., Wang, X., Yao, R., Wu, J., Xing, W., et al. (2025) · bioRxiv · doi:10.1101/2025.09.12.675839
Lee, K., Kim, M., Lim, S. O., Shin, D.-J., Shin, Y., Choi, J.-J., Lee, J. W., Kang, H. J., Lee, J. W., & Lee, K. (2025) · Biofabrication · doi:10.1088/1758-5090/ae26cc
“Briefly, raw sequencing data in FASTQ files were aligned to the human GRCh38 reference genome using BWA-MEM [20].”
PARTAGE: Parallel analysis of replication timing and gene expression
Murari, L. S. S., Dickinson, Q., Meyer-Nava, S., & Rivera-Mulia, J. (2025) · bioRxiv · doi:10.1101/2025.09.02.673838
Wang, K., Zhu, Y., Tian, Y., Qin, J., Wang, Z., Zhang, G., Wang, L., Zhang, Y., Yuan, H., Sun, N., et al. (2025) · Pharmacogenetics and Genomics · doi:10.1097/fpc.0000000000000575
“Alignment of processed reads against the human reference genome (build GRCh37/hg19) was performed with the Burrows-Wheeler Aligner software package (BWA release 0.7.15) under standard alignment configurations [33].”
InfluentialXiao, T., Wang, X.-F., Wang, Z., & Yan, H. (2025) · DNA Research · doi:10.1093/dnares/dsaf022
“7.17-r1188, 39 and the percentage of mapped reads was summarized with the function ‘stats’ in BamTools v2.”
InfluentialTian, T., Huang, C., & Li, L. (2025) · Pediatric Discovery · doi:10.1002/pdi3.70027
“7.10) [25] and duplicates removed with PICARD (v2.”
InfluentialWu, Y., Wang, W.-Q., Zhou, W., Ye, B.-Y., Chen, L., Tang, P., Niu, J.-M., Han, X., Sun, X.-F., Qin, S., et al. (2025) · Gene · doi:10.1016/j.gene.2025.149786
Hunt, B. J., Singh, K. S., Troczka, B. J., Mackisack, J., Randall, E. L., Mallott, M., Baril, T., Galbraith, J. D., Kuijper, B., Nauen, R., et al. (2025) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2025.104403
Pérez-Flores, O., Branstetter, M., Longino, J., Matos-Maraví, P., Borovanská, M., & Janda, M. (2025) · Insect Systematics and Diversity · doi:10.1093/isd/ixaf035
Li, W., Liu, M., Wu, L., Zhu, B., Li, X., Yang, Z.-Y., Liang, Y., & Lin, J.-Q. (2025) · Clinical and Translational Oncology · doi:10.1007/s12094-025-04021-w
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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