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###Getting started
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git clone https://github.com/lh3/bwa.git
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cd bwa; make
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./bwa index ref.fa
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./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
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./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
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###Introduction
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BWA is a software package for mapping low-divergent sequences against a large
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reference genome, such as the human genome. It consists of three algorithms:
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BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina
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sequence reads up to 100bp, while the rest two for longer sequences ranged from
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70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as the support of
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long reads and chimeric alignment, but BWA-MEM, which is the latest, is
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generally recommended for high-quality queries as it is faster and more
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accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp
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Illumina reads.
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For all the algorithms, BWA first needs to construct the FM-index for the
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reference genome (the **index** command). Alignment algorithms are invoked with
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different sub-commands: **aln/samse/sampe** for BWA-backtrack,
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**bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.
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###Availability
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BWA is released under [GPLv3][1]. The latest souce code is [freely
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available][2] at github. Released packages can [be downloaded ][3] at
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SourceForge. After you acquire the source code, simply use `make` to compile
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and copy the single executable `bwa` to the destination you want.
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###Seeking helps
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The detailed usage is described in the man page available together with the
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source code. You can use `man ./bwa.1` to view the man page in a terminal. The
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[HTML version][4] of the man page can be found at the [BWA website][5]. If you
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have questions about BWA, you may [sign up the mailing list][6] and then send
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the questions to [bio-bwa-help@sourceforge.net][7]. You may also ask questions
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in forums such as [BioStar][8] and [SEQanswers][9].
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###Citing BWA
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* Li H. and Durbin R. (2009) Fast and accurate short read alignment with
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Burrows-Wheeler transform. *Bioinformatics*, **25**, 1754-1760. [PMID:
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[19451168][10]]. (if you use the BWA-backtrack algorithm)
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* Li H. and Durbin R. (2010) Fast and accurate long-read alignment with
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Burrows-Wheeler transform. *Bioinformatics*, **26**, 589-595. [PMID:
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[20080505][11]]. (if you use the BWA-SW algorithm)
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* Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs
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with BWA-MEM. [arXiv:1303.3997v2][12] [q-bio.GN]. (if you use the BWA-MEM
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algorithm or the **fastmap** command, or want to cite the whole BWA package)
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Please note that the last reference is a preprint hosted at [arXiv.org][13]. I
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do not have plan to submit it to a peer-reviewed journal in the near future.
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[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
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[2]: https://github.com/lh3/bwa
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[3]: http://sourceforge.net/projects/bio-bwa/files/
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[4]: http://bio-bwa.sourceforge.net/bwa.shtml
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[5]: http://bio-bwa.sourceforge.net/
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[6]: https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
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[7]: mailto:bio-bwa-help@sourceforge.net
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[8]: http://biostars.org
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[9]: http://seqanswers.com/
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[10]: http://www.ncbi.nlm.nih.gov/pubmed/19451168
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[11]: http://www.ncbi.nlm.nih.gov/pubmed/20080505
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[12]: http://arxiv.org/abs/1303.3997
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[13]: http://arxiv.org/
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