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BWA specifications


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, Burrows-Wheeler Aligner (BWA)-MEM
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
  • sampe
  • samse




No version available



  • person_outline Richard Durbin

Additional information

Publications for Burrows-Wheeler Aligner

BWA citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] trimming was done with PRINSEQ-lite (version 0.20.4). Resulting high-quality reads were simultaneously mapped against the Mus musculus (GRCm38) and Drosophila melanogaster (dm6) reference genomes via BWA (version 0.7.15). SAMtools (version 1.4) was used to split the alignments into mouse and Drosophila reads. Read normalization via the Drosophila melanogaster spike-in material was carried out with […]


Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double strand breaks

Nat Commun
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] MiSeq reads of the cell-fusion (control) strain and 13 TAQed strains were mapped using BWA. Both whole-genome sequencing and tiling-array data were used to detect large-scale genome rearrangements and aneuploidies (Supplementary Fig. ). Chromosome-wide CNVs detected by both sequencing a […]


Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] equenced to 51 base pairs from both ends using the Illumina HiSeq 2000 in the Mayo Clinic Medical Genomics Core. Data were analyzed using the HiChIP pipeline. Briefly, paired-end reads were mapped by BWA and pairs with one or both ends uniquely mapped were retained. H3K4me3, H3K4me1, and H3K27ac peaks were called using the MACS2 software package at false discovery rate (FDR) ≤ 1%. SICER was used t […]


A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

Nat Commun
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] Sequence reads were processed and aligned to the reference genome (hg19) with the BWA algorithm and processed with Picard ( Polymorphic SNP and indel sites and genotypes were called with the HaplotypeCaller from GATK v3.1–. The HaplotypeCaller algorit […]


Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] The whole-genome-wide SNPs were identified using BWA (), SAMtools (), Picard Tools (, and the GATK toolkit (), according to the previously described pipeline method (). A total of 460 to 484 single-copy ortholo […]


Comparative whole genome re sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

PMCID: 5953909
PMID: 29766351
DOI: 10.1186/s12284-018-0224-3

[…] against the rice genome (16 pseudomolecules of cultivar Nipponbare, chromosome (Chr) 1 to 12, ChrUn, ChrSy, plastid, and mitochondrial genome contigs of MSU 7.0: by Burrows-Wheeler Aligner MEM (Li and Durbin ) ver. 0.7.12 with option of ‘–O 4′. This mapping condition was determined after comparisons under conditions with different gap penalty in a small batch pre […]


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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's avatar image

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