BWA protocols

BWA specifications

Information


Unique identifier OMICS_00654
Name BWA
Alternative names Burrows-Wheeler Aligner, BWA-MEM, BWA-SW, BWA-backtrack, MEM, ELM, Burrow-Wheelers Aligner, bwsmem, bwasw, SW
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data Short read alignment
Output format SAM
Biological technology Illumina, Oxford Nanopore
Operating system Unix/Linux
Programming languages C, Javascript
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.7.17
Stability Stable
Maintained Yes

Subtools


  • aln
  • sampe
  • samse

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Richard Durbin <>

Additional information


http://bio-bwa.sourceforge.net/

Publications for Burrows-Wheeler Aligner

BWA IN pipelines

 (1035)
2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] using the hiseq x ten illumina system sequencer with paired-end 150-bp read length and the mean average of 35–37x. bioinformatics analysis was performed as previously described34. briefly, the burrows-wheeler aligner (bwa-mem, version 0.7.7) was used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels […]

2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] illumina system sequencer with paired-end 150-bp read length and the mean average of 35–37x. bioinformatics analysis was performed as previously described34. briefly, the burrows-wheeler aligner (bwa-mem, version 0.7.7) was used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using […]

2018
PMCID: 5755806
PMID: 29304111
DOI: 10.1371/journal.pone.0190670

[…] reads were filtered. the filtered high-quality sequences were aligned and mapped onto the b73 reference genome (ftp://ftp.ensemblgenomes.org/pub/plants/release-24/fasta/zea_mays/dna/) using bwa software [18]. snp calling was performed using samtools software [18]. low-quality snps with a base quality value <20 and a read depth <4× the coverage from the gsh pool sequences […]

2018
PMCID: 5757203
PMID: 29379323
DOI: 10.2147/LCTT.S147841

[…] at ultra-high depth of 100,000× depth using illumina (san diego, ca, usa) hiseq 2500® instrument., the raw fastq sequences obtained were aligned to human reference genome (grch37/hg19) using bwa program32,33 and processed using picard and gatk toolkits.34,35 the low frequency variants were identified using lofreq program. an in-house method has been developed to filter the low frequency […]

2018
PMCID: 5760544
PMID: 29317692
DOI: 10.1038/s41598-017-18358-y

[…] and subjected to paired-end 101-bp sequencing on an illumina hiseq 2500 platform (san diego, ca, usa)., paired-end reads were mapped against the human reference genome (hg19, grch37) using bwa software (0.7.12). picard tools were used to remove pcr-duplicated and multiple aligned reads. after filtering out low-quality reads with mapping quality < 13 and base quality < 13, snp […]

BWA institution(s)
Broad Institute of Harvard and MIT, Cambridge, MA, USA
BWA funding source(s)
Supported by NIH 1U01HG005208-01.

BWA reviews

 (3)
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Arup Ghosh

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Desktop
Easy to use and fast short read aligner for ChIP-seq, RNA-seq, Variant calling and other NGS data.

Francois Sabot

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Desktop
We use BWA on a daily-basis and its results are always reliable and trustable.
We tested it in ALN/SAMPE legacy version and in MEM, and used those two versions depending the objectives.
The options are clear, tool is easy to use and efficient