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Burrows-Wheeler Aligner BWA

Alternative name: BWA-MEM | BWA-SW | BWA-backtrack | MEM | ELM

Maps low-divergent sequences against a large reference genome, such as the human genome. BWA consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

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3 user reviews

3 user reviews

Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

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's country flag

Francois Sabot

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

Joseale Romero's avatar image Joseale Romero's country flag

Joseale Romero

Good short read alignment. Fairly easy to use.

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BWA classification

BWA specifications

Software type:
Restrictions to use:
Output data:
Short read alignment
Biological technology:
Illumina, Oxford Nanopore
Programming languages:
C, Javascript
Computer skills:
Command line interface
Input format:
Output format:
Operating system:
GNU General Public License version 3.0


  • mem
  • aln
  • samse
  • sampe
  • index
  • bwasw

BWA distribution


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BWA support



  • Richard Durbin <>

Additional information

(Li, 2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.


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Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK

Funding source(s)

Wellcome Trust 077192/Z/05/Z

Link to literature

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