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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“7.17-r1188; Li and Durbin 2010) with default parameters.”
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“1 (Li & Durbin, 2010).”
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“0, Release 7; Kawahara et al., 2013) using BWA (Li & Durbin, 2010).”
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“7.17-r1188, 34 with parameters tuned for ancient DNA: -l 1024 -n 0.01 -o 2.”
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“The qualified reads were aligned with the soybean reference genome of the cultivated variety Williams 82 ( Wm82.a2.v1 ), which was downloaded from Phytozome ( h t t p s : / / p h y t o z o m e - n e x t . j g i . d o e . g o v / ) , with BWA software (Li and Durbin 2010 ).”
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“7.17) [23] to determine the genomic positions of eccDNA.”
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“3 [23].”
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“Read mapping was performed using BWA-MEM (Li and Durbin 2010) with the − 5SP and -t 8 options for alignment.”
Deconvolution-based Assessment of Fast and Slow Transcriptomic Components and Cellular Composition of Human Skeletal Muscles Using CAGE-seq Data
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“Alignment was performed against the human reference genome GRCh38 using a combination of bwa and HISAT2 programs, which allowed precise determination of transcription initiation sites (Li and Durbin, 2010; Kim et al., 2019).”
Discovery of a novel non-race-specific adult-plant resistance (APR) locus conferring stripe rust immunity in spelt wheat and its suppression in bread wheat
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“Reads were aligned to the spelt reference genome PI190962 and to an in-house HiFi whole-genome assembly of CDC Silex (C. Pozniak, unpublished) using Burrows– Wheeler Aligner (BWA) (Li and Durbin 2010).”
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“13 reference genome using BWA-MEM and duplicates marked using Picard(37,38).”
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“Sequencing reads were aligned to the WT reference sequence using the BWA-192 MEM aligner (v.0.7.17, (Li and Durbin, 2010)), then sorted and indexed using the SAM tools package (v.1.16.1 (Li et al. , 2009)).”
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“7.17-r1188 [22] with default settings.”
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“7.17) (Li and Durbin 2010).”
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“2 [29] using the Burrows-Wheeler Alignment (BWA-MEM) algorithm (BWA v.0.7.17) [30].”
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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: 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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