BWA protocols

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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



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  • person_outline Richard Durbin <>

Additional information

Publications for Burrows-Wheeler Aligner

BWA in pipelines

PMCID: 5754119
PMID: 29300782
DOI: 10.1371/journal.ppat.1006750

[…] reference genome (hbv genotype d3, genbank accession x65257; revised cambridge reference sequence for human mtdna, genbank accession number, nc_012920) using a network-aware version of the burrows-wheeler aligner [] ( with distance, gap and seed parameters as previously described []. duplicates were removed based on 5’ and 3’ positions […]

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 described. 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 ( indels […]

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 ( using bwa software []. snp calling was performed using samtools software []. low-quality snps with a base quality value <20 and a read depth <4× the coverage from the gsh pool sequences […]

PMCID: 5756397
PMID: 29304727
DOI: 10.1186/s12864-017-4416-9

[…] pools of the 42 populations comprising in total 425 individuals were resequenced with 20x target coverage. the sequence reads were aligned to the chicken reference genome (galgal4) [] using burrows-wheeler alignment algorithm implemented in bwa [] and sorted using samtools []. picard tools were used to mark duplicates and gatk was used for calling the snps [, ]. for more details […]

PMCID: 5758599
PMID: 29354142
DOI: 10.3389/fpls.2017.02185

[…] failed illumina's “chastity filter” were removed from raw fastq files. remaining reads were aligned to the malus × domestica v1.0 pseudo haplotype reference sequence (velasco et al., ) using the burrows-wheeler aligner tool v0.7.12 (li and durbin, ) and the tassel version 5 pipeline (glaubitz et al., ). tassel parameters included a minkmerl of 30, mnqs of 20, mxkmernum of 50000000 […]

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BWA in publications

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

[…] 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 […]

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

[…] of parental haploid strains were determined as the reference sequences for mapping and variant detection. the sequenced reads of taqed strain genome were mapped using a burrows–wheeler aligner (bwa), and small variants were called using the genome analysis toolkit (gatk). for arabidopsis, the genome sequence uploaded onto the tair10 database ( was used […]

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

[…] 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 […]

PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] the exome library was performed using the 100 bp paired-end mode of the truseq rapid pe cluster kit and truseq rapid sbs kit (illumina)., sequence reads were mapped to the human genome (hg19) using burrows-wheeler alignment tool. duplicate read removal was performed using picard and samtools, and local alignment was optimized by the genome analysis toolkit. variant calling was only performed […]

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

[…] mentioned above. all samples and data were collected with informed consent under local irb-approved protocols., 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 […]

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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

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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