BWA specifications


Unique identifier OMICS_00654
Name BWA
Alternative name Burrows-Wheeler Aligner
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


  • aln
  • samse
  • sampe



Add your version



  • person_outline Richard Durbin <>

Additional information

BWA articles

BWA citations

PMCID: 5940699

[…] was performed at the cnag using standard illumina protocols (barcelona, spain)., all raw sequence reads were mapped to the draft genome of the cynomolgus macaque macfas5 reference sequence using bwa-mem 0.7.5a-r405 with default parameters. picard tools ( were used to mark and remove pcr duplicates and to aggregate alignments and generate a single bam […]

PMCID: 5930415

[…] performed for illumina raw reads applying trimmomatic [9](version 0.32, parameters: illuminaclip off, slidingwindow 4:15, leading 3, trailing 3, crop off, headcrop off, minlen 36, avgqual off) using bwa-sw (version 0.7.13-r1126, default parameters) [10]. isolates generating a high number of ambiguous sites (cutoff: ≥15% “n” in the consensus sequence) were excluded from the mapping and tree […]

PMCID: 5927400

[…] script ( was used to separate reads by barcodes using a one mismatch threshold. cutadapt v1.8.1 software was applied to trim the adapters [24]. bwa aln version 0.7.8 [25] with the non-default parameters -l 16500 -n 0.01 -o 2 -t 2 was used to map the reads against the reference human genome (built 19). genotyping results and coverage […]

PMCID: 5928087

[…] and sequenced in 100-bp paired-end mode of the truseq rapid pe cluster kit and truseq rapid sbs kit (pe-402-4001, illumina). exome sequencing reads were mapped to the hg19 reference genome using burrows-wheeler aligner (bwa-0.7.5a)44. pcr duplicates were removed by picard-1.93 ( the mapped reads near putative indels were realigned and base quality […]

PMCID: 5938052

[…] with 151-bp paired-end reads. the paired reads were then aligned to the human reference genome (ucsc hg19, ncbi build 37.1) using the burrows–wheeler aligner (bwa; version 0.7.10) ( pcr duplications were removed using picard (version 1.118) ( the genome analysis toolkit (gatk; version 3.2-2) […]

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

BWA reviews

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Arup Ghosh

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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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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