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
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Figures
![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)
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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
Research works printed but not linked: 1
- Burrows, 1994, A block-sorting lossless data compression algorithm
Cited by
Sorted by citations
Items 901–1,000 of 1,225
Tan, Y., Lim, P., Yeap, S., Prasedya, E., Poong, S.-W., Brodie, J., Cottier-Cook, E. J., Roleda, M. Y., & Liu, T. (2026) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2026.108688
Emergence of Reassortant Crimean-Congo Hemorrhagic fever virus lineages, Pakistan, 2023-2024.
Umair, M., Jamal, Z., Ali, Q., Hakim, R., Rana, M. S., Javed, Y., Bugti, A. R., Ayub, A., Sabeen, F., Waheed, Y., et al. (2026) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2026.105988
3D Epigenomic Remodelling Mediated by Foxa1 Drives Gemcitabine Resistance in Pancreatic Cancer.
Wang, X.-L., Cao, Y.-L., Gu, J., Qi, T., Guo, J., Yang, Y.-J., Tang, H., Shen, T., Wang, Q., Cao, X., et al. (2026) · Cancer Letters · doi:10.1016/j.canlet.2026.218721
Integrative multi-omics analysis of growth plate regulation underlying body size in miniature pigs
Khaveh, N., Berghöfer, J., Ralph, B., Buschow, R., Cirksena, K., Drögemüller, C., Fatima, A., Grabert, G., Gerold, G., Grahofer, A., et al. (2026) · Communications Biology · doi:10.1038/s42003-026-10538-9
“Processed reads were aligned to the autosomal Sus scrofa 11.1 reference genome (Ensembl) using the Burrows-Wheeler Aligner (BWA) v. 0.7.17-r1188 76 .”
InfluentialUnravelling Past Population Events in Diatoms With Genomic Based Demographic Inferences
van Dijk, R. L., Suárez-Menéndez, M., Postel, U., Bérubé, M., Beszteri, B., & Palsbøll, P. (2026) · Marine Ecology · doi:10.1111/maec.70108
“2/3rd of the observed sites were used to create a subsample functioning as an SFS testing set, replacing the SFS bootstrapping, to infer confidence intervals (Li and Durbin 2010).”
Zhang, B., Lin, Y., Xie, S.-Y., Zhu, X.-H., Zhang, X.-P., Hu, L.-Y., Qiu, M., Lee, H.-K., Shen, C.-Y., You, M.-L., et al. (2026) · BMC Biology · doi:10.1186/s12915-026-02665-w
“The sequence reads were mapped to the genome (hg38) using BWA-MEM [69].”
Kisoi, G., Bargul, J., Kinyua, J., Langat, S. K., Koka, H., Lutomiah, J., & Eyase, F. (2026) · bioRxiv · doi:10.64898/2026.06.25.734443
“Quality reads were aligned to the genome of host species and humans using BWA [36] for removal of host sequences.”
Eleazer, R., George, S., Shoemaker, L. J., Saintilnord, W. N., Cassidy, R. N., Pyman, A., Lau, K. H., Soper-Hopper, M. T., Lee, H., Chandler, D. P., et al. (2026) · Cell Communication and Signaling · doi:10.1186/s12964-026-03021-9
“1.19), and then the remaining sequences aligned to the hg38 reference genome using the BWA algorithm [73] (mem mode; default settings).”
InfluentialKaur, P., Hasib, T. K., Kaur, S., Sharun, Bhatia, P., Trehan, A., Sachdeva, M., Sreedharanunni, S., & Singh, M. (2026) · Molecular Biology Reports · doi:10.1007/s11033-026-12147-5
“The sequences obtained were aligned to human reference genome (GRCh37/hg19) using BWA program and analysed using Picard and GATK version 3.6 to identify variants relevant to the clinical indication [18–21 ].”
InfluentialInvestigating ancient human DNA preservation on cave walls and in rock art
Mesa, A. B., Essel, E., Jáuregui, L., Galtier, A., Zavala, E. I., Nota, K., Szymanski, M., Zorn, J., Gomes, H., Nash, G., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74234-2
“…classi fi er KrakenUniq 64 , bins sequences by mammalian biological families and maps them to their best matching reference genome within each family using BWA 65 , or in the case of sequences identi fi ed as Homini-dae , to the revised Cambridge reference sequence of the human mtDNA genome 61 .”
Carroll, K. N., Lesseur, C., Brunst, K., Colicino, E., Chiu, Y., Hartman, T. J., Coull, B., & Wright, R. J. (2026) · Placenta · doi:10.1016/j.placenta.2026.06.013
Li, K., Wu, N., Hu, J.-H., Hu, X.-C., Tang, H.-Y., Xu, W., Dong, Z.-Q., Lai, X.-D., Xu, L.-H., Fu, C., et al. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.6c03658
Koloi, S., Mehla, K., Ganguly, I., Singh, S., & Dixit, S. (2026) · The Nucleus · doi:10.1007/s13237-026-00692-0
Guha, P., Hake, A. A., Barbadikar, K. M., Gopi, P., Magar, N. D., Balija, V., Gokulan, C., Kommana, M. L., Jamaloddin, M., Sharma, A., et al. (2026) · Journal of Crop Science and Biotechnology · doi:10.1007/s12892-026-00363-1
“ASM465v1.dna. toplevel.fa.gz ) reference genome using BWA tool (Li and Durbin 2010 ), and variant calls generated with with bcftools v1.”
A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata
Zhang, F., Yang, Y., Li, W., Shi, C., Zhu, X., & Gao, L.-Z. (2026) · bioRxiv · doi:10.64898/2026.04.28.721348
Honarmand, H., Babaei, S., Bonyadi, M. J., & Barzegar, M. (2026) · Journal of Neurogenetics · doi:10.1080/01677063.2026.2687566
Chaudhary, A., Lin, X., Vitaterna, M., Auch, B., Liachko, I., & Green, S. (2026) · Microbiology Resource Announcements · doi:10.1128/mra.01047-25
Li, L., Saw, T. Y., Chou, N., Goh, J. L. J., Kwa, J. E., Chock, W. K., Singhal, V., Li, Z., Huang, M. J., Ng, H., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-74320-5
Wang, R.-F., Huang, L., Umer, M., Yu, Q.-X., Liu, Q., Lu, Q., Liu, H., Li, H.-F., Li, S.-X., Hong, Y.-B., et al. (2026) · BMC Plant Biology · doi:10.1186/s12870-026-09138-w
“The Burrows-Wheeler Aligner (BWA) software [21] was employed to align the clean reads to the reference genome of Arachis hypogaea var.”
Self-citationA foundational quantum framework for multi-pattern string matching in k-mer detection
Papalitsas, C., Mouratidis, I., Patsakis, M., Stogiannos, E., Georgakopoulos-Soares, I., & Koulouras, G. (2026) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2026.1802517
“…for memory-efficient querying (Melsted and Pritchard, 2011; Chikhi and Rizk, 2013), and FM-index/BWT-derived compressed indexing (Li and Durbin, 2009; Li and Durbin, 2010), achieve near-linear or sub-linear performance in practice and represent the current benchmark for large-scale k-mer analysis.”
Improved chromosome-level genome assembly of Pleurotus ostreatus CCMSSC 00389
Ma, Y.-J., Huang, C.-Y., Zhao, M.-R., Wu, Z., Yao, F.-J., & Zhang, L.-J. (2026) · G3 · doi:10.1093/g3journal/jkag150
“BWA was used for reads alignment (Li et al. 2010).”
Priyono, D. S., Prakarsa, T. B. P., Eprilurahman, R., Arisuryanti, T., Ula, A. L., Abdul‐Latiff, M. A. B., & Rahayuningsih, M. (2026) · Scientific Reports · doi:10.1038/s41598-026-57251-5 · Cited by 1
Expanding the Spectrum of BCAP31-Associated Diseases
Ishiguro, M., Funayama, M., Park, D. H., Hatano, T., Nakazato, T., Luo, Y., Osawa, M., Li, Y., Yoshino, H., Hattori, N., et al. (2026) · Neurology: Genetics · doi:10.1212/nxg.0000000000200404
Yin, H., Ge, Q.-Y., Wang, Z., Bi, C.-W., & Dai, X.-G. (2026) · Journal of Forest Research · doi:10.1007/s11676-026-02089-w
“The clean reads from each sample were then aligned to the M. biondii reference genome (Dong et al. 2021) using BWA-MEM (Version 0.7.15) with default parameters (Li et al .”
InfluentialThe price of survival: comparative adaptation to high altitudes between yaks and cattle
Tan, L., Liu, X.-J., Ma, Y.-G., Yang, J.-F., Zhang, Q.-Y., Zhang, J.-B., Bai, B.-Q., Ma, H., Meng, R., Degen, A., et al. (2026) · Animal Microbiome · doi:10.1186/s42523-026-00584-3
“The filtered reads were matched with the reference genome using BWA (v.0.7.17, r1188) [41] at default settings.”
InfluentialWang, M., Jiang, J.-W., Liang, H., Lei, L., Chen, Y., Li, Y.-S., Hua, Y., Ma, T., Ding, W.-N., Li, X., et al. (2026) · Frontiers in Plant Science · doi:10.3389/fpls.2026.1864920
“Then, we obtained mitochondrial-related scaffolds and polished these scaffolds by BWA and Pilon to correct any erroneous bases or indels (Li and Durbin, 2010; Walker et al., 2014).”
Liu, F.-L., Chen-Zhang, Y., Huang, J.-M., Jiang, Q., Liu, J., & Yang, J.-Y. (2026) · Functional & Integrative Genomics · doi:10.1007/s10142-026-01896-y
“Reads were aligned to the human reference genome (GRCh37/hg19) using the Bur - rows-Wheeler Aligner (BWA) (Li and Durbin 2010 ).”
Lu, S. (2026) · BMC Plant Biology · doi:10.1186/s12870-026-09180-8
“The transcriptome data were mapped to the mitogenome using BWA [26].”
Evolution of supernumerary chromosomes in wheat blast fungal pathogens
Cruppe, G., Bika, R., Lin, G., Calderon, L., Montano, J. A. C., Suetler, T., Stack, J., Koo, D., Asuke, S., Tosa, Y., et al. (2026) · bioRxiv · doi:10.64898/2026.06.01.729302
“BWA was used to align clean reads to the B71 reference genome (B71v2) 17,18,54 .”
Higashiyama, R., Yoshida, T., Shiraishi, K., Miyakoshi, J., Torasawa, M., Shirasawa, M., Masuda, K., Shinno, Y., Matsumoto, Y., Okuma, Y., et al. (2026) · British Journal of Cancer · doi:10.1038/s41416-026-03457-3
“The resulting libraries were subjected to paired-end sequencing with 75-bp reads on the HiSeq 2500 (Illumina) or 150-bp reads on the NovaSeq 6000 system (Illumina).”
Yang, B., Li, F., Zhang, Y., Zhang, F., Wang, Z., Da, Y., Yang, X., Xing, W., & Tian, J. (2026) · Communications Biology · doi:10.1038/s42003-026-10320-x
Pellegrinetti, T., Hammond, C., Pérez-López, E., Muirhead, K., Bennypaul, H., Sanderson, D., & Dumonceaux, T. J. (2026) · Microbial Genomics · doi:10.1099/mgen.0.001748
“7.17-r1188 [27] with a reference database prepared from the previously reported milkweed yellows genome (GCA_000309485).”
InfluentialFrom Laboratory to Real Clinical Practice: A Multidisciplinary Approach Towards the Next Probiotics
Pavoni, M., Fiorini, G., Saracino, I., Gatta, L., Manta, R., Holton, J., Figura, N., Massarenti, G., Leo, C., Rosa, B., et al. (2026) · Antibiotics · doi:10.3390/antibiotics15060595
“7.17 [16].”
InfluentialErdenechuluun, J., Gombojav, B., Batsaikhan, T., Lu, Y.-S., Danshiitsoodol, N., Makhbal, Z., Jargalmaa, M., Jargalkhuu, T., Hsu, H., Lin, P.-H., et al. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27125364
“Raw reads were aligned to the human reference genome (hg38) using BWA (version 0.7.17) [76].”
InfluentialChigira, K., Yamamoto, E., Goto, A., Ikegaya, T., Suzuki, N., Kawahara, Y., Yamasaki, M., Sugimoto, K., & Hori, K. (2026) · Breeding Science · doi:10.1270/jsbbs.25062
“0 in BWA software version 0.7.17 (Li and Durbin 2010).”
InfluentialZhang, J., Li, Y., Li, Y., Zhang, J.-M., Robbeets, M., Ning, C., Wang, Y., & Wang, H. (2026) · Archaeological Research in Asia · doi:10.1016/j.ara.2026.100709
Paleogenomes reveal the evolutionary relationship between modern and cave lions
Stanton, D. W. G., Bergström, A., Heintzman, P. D., van der Valk, T., Carmagnini, A., Ersmark, E., Pawar, H., Sandoval‐Velasco, M., Androsov, S., Fedorov, S., et al. (2026) · Cell · doi:10.1016/j.cell.2026.05.007
Eemian palaeogenetics demonstrates loss of diversity in modern fallow deer (Dama dama)
Rocha-Méndez, A., Arnold, P., Kindler, L., Gaudzinski-Windheuser, S., Roebroeks, W., Scherjon, F., & Hofreiter, M. (2026) · iScience · doi:10.1016/j.isci.2026.116204
Wang, M., Lv, S., Gao, S.-Y., Liu, L., Wu, X.-K., Liu, Y.-L., Li, D., Jin, G., & Ma, P.-F. (2026) · The Plant Journal · doi:10.1111/tpj.70965
Zhou, X., Li, H.-X., Yang, X., Wang, C.-L., & Zhang, W.-T. (2026) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.70249
“The paired-end reads were aligned to the Ensembl GRCh37/hg19 human reference genome using the Burrows-Wheeler Aligner (BWA) software (Li and Durbin 2010).”
Self-citationYosifov, D., Robrecht, S., Giza, A., Maity, P., Riecke, A., Schneider, C., Jebaraj, B., Dheenadayalan, R. P., Jumaa, H., Young, M., et al. (2026) · HemaSphere · doi:10.1002/hem3.70385
A chromosome-level genome assembly of the endangered rose Rosa anemoniflora
Zhou, X.-Z., Yu, Q., Fu, C., Lin, G., Huang, X., Kang, T., & Gao, W. (2026) · Scientific Data · doi:10.1038/s41597-026-07516-5
Makale, K. P. P., Kampouris, I. D., Ultra, V. U., Dineo, O., Babin, D., & Rantong, G. (2026) · bioRxiv · doi:10.64898/2026.05.29.728080
“Following the assembly, the contigs were mapped to the reads using NGLess (v.1.5) (Coelho et al. 2019) and BWA-MEM (v.0.7.17) (Li and Durbin 2010).”
InfluentialEvaluating relationship inference from low-quality DNA using a conditional simulation framework
Jepsen, A. H., Kampmann, M., Tillmar, A. O., Børsting, C., Andersen, J., & Kling, D. (2026) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2026.103541
Luo, W., Liang, Y., Lin, Q., Liu, H., Ling, S., Shi, Y., Zhou, B., Shen, Z., Wang, J., Niu, J., et al. (2026) · The Plant Journal · doi:10.1111/tpj.70953
Makarik, T., Nikulina, E., Treglasova, S., Stepanova, E., Chernova, N., Biderman, B., Kokhno, A., & Sudarikov, A. (2026) · Diseases · doi:10.3390/diseases14060190
Extinct Dalian horse as a genetic bridge between Late Pleistocene North American and Eurasian equids
Song, S., Xiao, B., Xing, F., Qi, L., Bao, L., Hou, Y., Zhang, Y. X., Zheng, M., Hu, J., Zheng, L., et al. (2026) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2026.0314
Gao, J., Jiang, J., Tao, Q.-C., Haider, S., Zhang, S., Zhang, Z., Liu, X., Ni, D.-A., Qin, Q.-P., & Fan, M. (2026) · Euphytica · doi:10.1007/s10681-026-03752-3
“The Burrows-Wheeler Aligner (BWA, Version 0.7.12) (Li and Durbin 2010) was used with default parameters to align the clean reads to the H. citrina reference genome (GenBank accession: GCA_017893485.”
InfluentialMiao, J.-S., Zhang, C., Jiang, Q., Yao, Z.-L., Cao, K., Chen, J., Wang, H., & Liu, N. (2026) · Environmental Microbiology Reports · doi:10.1111/1758-2229.70366
“The clean reads of each sample were then mapped to the genome assembly of strain Xianghu001 using bwa mem (version 0.7.17-r1188) with default parameters (Li and Durbin 2010).”
InfluentialWen, Z., Chen, S.-S., Chen, H.-J., Liu, X.-T., Qi, X., Feng, J., Jin, Y., Sun, M., & Deng, Y.-M. (2026) · BMC Plant Biology · doi:10.1186/s12870-026-09074-9
“7.15) [54]. alignment of interspecies sequences using MAFFT v7.”
InfluentialKuo, C.-Y., Cheng, W.-C., & Wu, Y.-C. (2026) · International Symposium on Circuits and Systems · doi:10.1109/iscas66217.2026.11562281
Stepwise construction of the path to doubled haploid breeding in sorghum
Sui, Y., Sun, Y., Cheng, Z.-X., Li, Y., Li, K., Zhang, X., Yin, T., Yang, S.-M., Li, G.-Y., Liu, M.-X., et al. (2026) · Science Advances · doi:10.1126/sciadv.aed5464
Variantes germinales en pacientes con cáncer gástrico esporádico del suroccidente colombiano
Rojas, S. C. R., Rosero, E. M. B., Bedoya, A. M. C., & Galindo, C. Y. R. (2026) · Revista Colombiana de Gastroenterología · doi:10.22516/25007440.1511
Population Structure of the Jewel Scarab Chrysina gloriosa
Sylvester, T., Hjelmen, C. E., Thompson, M. J., Blackmon, L. T., Alfieri, J. M., Hoover, Z., Esfandani, T., & Blackmon, H. (2026) · Genome Biology and Evolution · doi:10.1093/gbe/evag123
“We indexed the C. gloriosa genome (containing both nuclear and mitochondrial genomes) using the faidx module of SAMtools version 1.14 and the index module of BWA version 0.7.17 (Li and Durbin 2009, 2010; Li 2013).”
InfluentialXu, X., Zeng, J., Li, H., Cotton, A. M., Liang, D., Hu, S.-J., & Zhang, P. (2026) · BMC Genomics · doi:10.1186/s12864-026-12955-w
“Illumina short reads were mapped to the P. bootes reference genome using BWA (version 0.7.17-r1188) [82] with default parameters.”
InfluentialSelf-citationChromosome-level genome assembly of Xuefeng Black-bone chicken and comparative genomics analysis
Guo, S., Huang, J.-Z., Zi, Q., Li, P., He, L., He, X., Zhang, H.-H., Li, D., Li, M., Qu, X., et al. (2026) · BMC Genomics · doi:10.1186/s12864-026-12952-z
“Subsequently, all clean Illumina short reads were mapped to the assembled genome using BWA software [19, 20] to assess the consistency of the genome.”
Peng, Z., Li, R., Dao, W., Li, X., Xiong, C.-Y., & Han, R. (2026) · Scientific Data · doi:10.1038/s41597-026-07451-5
Protective TMEM106B-rs3173615 delays age at onset in GRN mutation carriers
Pagano, L., Saraceno, C., Geviti, A., Fostinelli, S., Facconi, A., Laganà, V., Giacomucci, G., Cotelli, M. S., Ingannato, A., Bagnoli, S., et al. (2026) · Molecular Psychiatry · doi:10.1038/s41380-026-03653-w
“The remaining high-quality reads were then aligned to the hg38 reference genome using BWA-MEM (version 0.7.17-r1188) [34].”
InfluentialGenomic insights into the probiotic potential of Bacillus velezensis D-18 for aquaculture
Monzón-Atienza, L., Felipe, Á. L., Cabrera-Guerle, N., Gómez-Mercader, A., Carlino-Costa, C., Ramos-Vivas, J., Zhang, M.-L., Montero, D., Acosta, F., & Galindo-Villegas, J. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1824441
“7.17) (Li and Durbin, 2010), and duplicate reads were removed with Sambamba (v0.”
InfluentialXu, K., Zhang, K., Li, J., Huang, Y.-X., Gou, J., Zhou, J.-L., Wang, Y., Chen, F.-F., & Xiao, P. (2026) · BMC Genomics · doi:10.1186/s12864-026-12943-0
“7.17 [15].”
InfluentialUprety, T., Goehring, L., Rozhbayani, A., Meyer, A., Todd, S., Abdelrazek, S., Lahmers, K., & Erol, E. (2026) · Microbiology Resource Announcements · doi:10.1128/mra.01347-25
Gwayi, S., Tomoka, T., Chimusa, E. R., Fedoriw, G., & Kumwenda, B. (2026) · African Journal of Laboratory Medicine · doi:10.4102/ajlm.v15i1.3073
“28 Variant calling was performed on recalibrated bases via Genome Analysis Toolkit Haplotype Caller, followed by joint genotype calling on the individual sample generating a genotype Variant Call Format file.”
A novel hemizygous missense variant in the BEND2 gene is associated with nonobstructive azoospermia
Luo, C.-H., Yu, Z.-Q., Wang, H.-Y., Zhou, H., Wu, Y.-H., Shao, L.-F., Liu, H.-C., Zhan, J.-F., Xie, C., Ke, S.-W., et al. (2026) · Asian Journal of Andrology · doi:10.4103/aja2025122
Gil-Polo, A., Bledsoe, R. B., Calvert, M. B., Cherry, L., Epstein, B., Fudge, R., Harris, J. E., Tiffin, P., & Burghardt, L. (2026) · mBio · doi:10.1128/mbio.03793-25
“7.17; [37]; NCBI BioProject: PRJNA388336).”
InfluentialZhang, N., Li, L., Ta, K.-W., Shi, C., Seim, I., Zhang, Y., Zhang, W.-J., Cui, Z., Xiang, X., Jia, L.-M., et al. (2026) · bioRxiv · doi:10.64898/2026.05.06.723128
A chromosome-level whole genome of Red mahseer (Tor sinensis)
Que, Y.-F., Li, W.-T., Wu, J., Hu, X.-K., Wang, E., Dong, W.-W., & Zhu, B. (2026) · Scientific Data · doi:10.1038/s41597-026-07385-y
“Scaffolding was performed using the 3D-DNA pipeline 22,23 , which clustered 158 contigs into 50 chromosome-scale groups.”
Telomere-to-telomere Genome Assembly of Equus kiang (Tibetan wild donkey)
Zheng, Y., Hu, Y., 索佳佳, Wang, W., Wang, Y., Cao, L., Sun, P., 张麦收, Zhao, M., Yang, W., et al. (2026) · Scientific Data · doi:10.1038/s41597-026-07355-4
“7.17) 36 .”
InfluentialClarke, S., Allen, I., Ravix, J., Marção, M., Carcanholo, F., Doughan, A., Sanchez-Covarrubias, A. P., Cornwall, D., Harrison, S., Volmar, C., et al. (2026) · Scientific Reports · doi:10.1038/s41598-026-51649-x
Ancient DNA reveals pig domestication history in Northeastern China
Tao, H.-L., Zheng, M., Xiao, B., Song, S.-W., Xing, F., Guan, R., Zhu, Y., Jiang, S., Lai, X.-L., Yuan, J.-X., et al. (2026) · Journal of Genetic Engineering and Biotechnology · doi:10.1016/j.jgeb.2026.100704
A retrospective analysis of cystic enteropathy in Alabama broilers
Lockyear, O., Álvarez-Narváez, S., Conrad, S. J., Carnaccini, S., Huber, L., & Walz, H. (2026) · Avian Pathology · doi:10.1080/03079457.2026.2651255
“7.17 (Li & Durbin, 2010), SAMtools V1.”
InfluentialMutational landscape in the precancerous stages of sporadic colorectal cancer.
Valíčková, A., Urbanova, M., Horák, J., Jungwirth, J., Kral, J., Hucl, T., Makajevová, V., Summerova, S., Kohout, P., Matěj, R., et al. (2026) · Oncology Letters · doi:10.3892/ol.2026.15634
Shifflett, S. A., Weyer, E., MacDonald, M. L., & Ellis, V. A. (2026) · Molecular Genetics and Genomics · doi:10.1007/s00438-026-02427-x
“Trimmed forward and reverse reads were mapped to the assembled eastern chipmunk reference genome using BWA mem v.0.7.17 (H. Li and R. Durbin 2009).”
InfluentialKhokhar, E. S., & Lozada, D. N. (2026) · G3 · doi:10.1093/g3journal/jkag116
“FASTQ files were aligned to the Zunla-1 ( C. annuum L.) reference genome (Qin et al. 2014) using the Burrows–Wheeler Aligner (Li and Durbin 2010).”
von Maydell, D., Schwerdt, J., Lehnert, H., Pöschl-Grau, Y., Schmutzer, T., & Marthe, F. (2026) · BMC Plant Biology · doi:10.1186/s12870-026-08853-8
“Trimmed reads were mapped against the ‘mock refer-ence’ using BWA-mem (Galaxy Version 0.7.18; [37, 38]).”
InfluentialLi, Z., Ren, M.-L., Hu, A., Meng, F.-F., & Wang, J.-J. (2026) · Molecular Ecology · doi:10.1111/mec.70367
“7.17) (Li and Durbin 2010), and SAMtools (v1.”
InfluentialSchramm, D., & Burg, T. (2026) · Ecology and Evolution · doi:10.1002/ece3.73650
“The reference genome was indexed using samtools 0.1.2 (Danecek et al. 2021) and the Burrows-Wheeler Alignment Tool (bwa) aligned the forward and reverse reads (Li and Durbin 2010).”
InfluentialEvolution of Resistance to Avian Malaria Infection in an Endemic Hawaiian Honeycreeper
Neddermeyer, J. H., Cassin‐Sackett, L., Paxton, E. H., Campana, M. G., Fleischer, R. C., & Foster, J. T. (2026) · Ecology and Evolution · doi:10.1002/ece3.73550
“Trimmed FastQ reads were aligned to the reference Oʻahu ʻamakihi genome using BWA-MEM 0.7.17 (Li and Durbin 2010).”
InfluentialGeviti, A., Pagano, L., Grassi, M., Saraceno, C., Facconi, A., Fostinelli, S., Laganà, V., Giacomucci, G., Cotelli, M., Cantoni, V., et al. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27094081
“Adapters and low-quality reads were filtered out using Trimmomatic (version 0.39) [37], while the remaining high-quality reads were mapped to the GRCh38/hg38 reference genome employing BWA-MEM (version 0.7.17-r1188) [38].”
InfluentialXu, M., Zhang, R., Fan, S.-Q., Sun, M., & Zhang, X. (2026) · Genes · doi:10.3390/genes17050565
“Sequence reads were then mapped to the reference human genome (GRCh38/hg38) using Burrows-Wheeler Aligner (BWA) software (v.0.7.17) [9].”
InfluentialChen, L., Zhang, B., Zhang, D.-X., Gao, S.-Z., Li, C.-X., Huang, X.-L., & Cui, Y.-Q. (2026) · Journal of Archaeological Science: Reports · doi:10.1016/j.jasrep.2026.105718
Ndou, M., Potts, W. M., Duong, T. A., Teske, P. R., Childs, A.-R., & Henriques, R. (2026) · Evolutionary Applications · doi:10.1111/eva.70247
Niu, Y., Wang, R., Wang, L., Huang, A.-Z., Han, X., Yu, R., Chen, S.-J., Wang, J.-T., Cheng, J.-W., Chen, C.-M., et al. (2026) · Journal of genetics and genomics = Yi chuan xue bao · doi:10.1016/j.jgg.2026.04.017
Identifying unknown contributors to two-person DNA mixtures via whole-genome sequencing.
Lei, Y.-T., Liu, Z., Han, S., Lin, X., Sun, Q., & Ou, X. (2026) · Forensic Science International: Genetics · doi:10.1016/j.fsigen.2026.103530
Genomic insights into the admixture history and adaptive evolution of the Zhuang people
Mao, C., Li, S., Lu, Y., Liu, Q., Deng, L., Gao, Y., Zhang, X., Chen, H., Yang, Y., & Xu, S. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag105
“Reads were merged, adaptors were trimmed, and sequences were mapped to the human reference genome (GRCh38) using the Burrows-Wheeler Aligner (Li and Durbin 2010).”
Grossfurthner, L. P., Islam-Faridi, N., Hohenlohe, P. A., Waits, L. P., & Richardson, B. (2026) · American-Eurasian journal of botany · doi:10.1002/ajb2.70206
Zhang, H.-L., Cui, W., Liu, Y.-L., Zheng, W., Zeng, Y.-H., Sun, M.-L., Li, Y., Deng, L.-Y., Zeng, H., Zhao, B.-Y., et al. (2026) · Plant Diversity · doi:10.1016/j.pld.2026.05.009
Wen, S.-L., Zhou, K., Min, Y., Yang, K., Shang, C.-Q., Peng, L., Cai, X.-W., Leng, Y.-X., Shen, L.-N., Deng, L., et al. (2026) · Horticulture Research · doi:10.1093/hr/uhag174
“7.18 [ 51] was first utilized to map the genomic sequencing data of each individual to the R. delavayi genome.”
InfluentialRorippa islandica: a genetically accessible dicot model system to study flooding tolerance
Bartylla, M. M., Düthorn, E. L. R., Müller, J., Wirtz, M., van Veen, H., Sasidharan, R., & Mustroph, A. (2026) · Plant Physiology · doi:10.1093/plphys/kiag254
“Reads were mapped to the reference transcriptome of R. island-ica with the Burrows–Wheeler Aligner maximal exact matches algorithm ( Li and Durbin 2010).”
Genomics Insights into the Demographic History and Introgression of Tibetan Pigs
Xue, P.-X., Zha, C.-W., Luo, Y.-B., Huang, N., Liu, N., Wang, H., & Fang, M.-Y. (2026) · Animals · doi:10.3390/ani16091328
“7.19) [18].”
InfluentialYerramilli, N. P., Hasan, F., Sanjeev, S., Kapoor, P., Rahman, K., & Kashyap, R. (2026) · International Journal of Molecular and Immuno Oncology · doi:10.25259/ijmio_29_2025
Liu, M., Du, M., Xi, Z., Tastambek, K., Bao, Y., Song, X.-T., Zhou, A.-N., & Wang, Y.-Y. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.00268-26
“1.2; https://github.com/voutcn/megahit) (38).”
InfluentialSilver-Gorges, I., Komoroske, L., Adkins, J. L., Swenson, J. D., Addison, D. S., Burkholder, D. A., Bagley, D., Goodwin, G. D., Hart, K. M., Pfaller, J. B., et al. (2026) · Conservation Genetics · doi:10.1007/s10592-026-01783-w
“7.17; Li and Durbin 2010).”
InfluentialFigueroa-Ildefonso, E., Cabrera-Sosa, L., Kattenberg, J. H., Valdivia, H., Delgado-Ratto, C., Rosanas-Urgell, A., & Gamboa, D. (2026) · Scientific Reports · doi:10.1038/s41598-026-48246-3
“The trimmed reads were competitively mapped against the reference genome of the P. falciparum 3D7 (v3) and human (GRCh38.p13) reference genomes, using BWA-MEM version 0.7.17 27 .”
InfluentialTorres, H. F., Esparraga-Calle, A. V., Ascue, F., Fernandez-Castro, P., Heredia-Vilchez, L. A., Gongora-Bardales, D. J., Villegas, S. M. P., Trigoso-Yalta, M. J., Zamora-Huamán, S. J., Portocarrero, T., et al. (2026) · Scientific Reports · doi:10.1038/s41598-026-48764-0
Metabolome Diversity Enhances Resistance of Intertidal Clams to Thermal Stress
Zhi, H., Wei, X.-T., Lin, X., Ma, L., Zhang, T., & Dong, Y. (2026) · Integrative Zoology · doi:10.1111/1749-4877.70107
Whole-exome sequencing identifies PRSS56 variants in Chinese patients with microphthalmia
Luo, J., Li, K., Yang, R., Tang, M., & Ge, J. (2026) · BMC Medical Genomics · doi:10.1186/s12920-026-02376-9
“Raw reads in FASTQ format were quality-filtered to generate clean reads and then aligned to the human reference genome (UCSC hg38) using the Burrows-Wheeler Aligner (BWA) [19].”
Dickinson, Q., Yu, C., & Rivera-Mulia, J. (2026) · bioRxiv · doi:10.64898/2026.04.16.719037
“Alignment: Following preprocessing, sequencing reads are mapped to the reference genome using the Burrows-Wheeler Alignment (BWA-MEM) tool [36].”
Igh nuclear speckle association promotes V(D)J recombination
Priyadarshi, S., Bhat, K. H., Drake, E. B., Naiyer, S., Farooq, H., Qu, X.-Y., Cantillo, J., Lei, X., Ermiş, E., Kleiman, E., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-71577-8
“The pipeline was set up with BWA (0.7.15-r1140) 80 to map each read end separately to the mm10 reference genome (GRCm38).”
InfluentialGe, D., Zou, R., Jin, J., Shi, X., Wang, X., Zhang, D., Zhang, X., Zhang, Q., & Ning, C. (2026) · Archaeological and Anthropological Sciences · doi:10.1007/s12520-026-02466-w
“7.12 with the parameters -n and -l set to 0.01 and 1024, respectively (Li & Durbin, 2010).”
InfluentialRomanenko, M. N., Shikov, A., Shmatov, F., Savina, I. A., Belousov, M., Solovchenko, A., Chivkunova, O., Savelev, G. K., Kuznetsova, I., Karlov, D., et al. (2026) · Microbiology spectrum · doi:10.1128/spectrum.02919-25
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
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
