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Heng Li 2014-05-14 14:33:42 -04:00
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README.md
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###Getting started ##Getting started
git clone https://github.com/lh3/bwa.git git clone https://github.com/lh3/bwa.git
cd bwa; make cd bwa; make
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./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz ./bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz ./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
###Introduction ##Introduction
BWA is a software package for mapping DNA sequences against a large reference BWA is a software package for mapping DNA sequences against a large reference
genome, such as the human genome. It consists of three algorithms: genome, such as the human genome. It consists of three algorithms:
@ -22,7 +22,7 @@ reference genome (the **index** command). Alignment algorithms are invoked with
different sub-commands: **aln/samse/sampe** for BWA-backtrack, different sub-commands: **aln/samse/sampe** for BWA-backtrack,
**bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm. **bwasw** for BWA-SW and **mem** for the BWA-MEM algorithm.
###Availability ##Availability
BWA is released under [GPLv3][1]. The latest souce code is [freely BWA is released under [GPLv3][1]. The latest souce code is [freely
available at github][2]. Released packages can [be downloaded][3] at available at github][2]. Released packages can [be downloaded][3] at
@ -30,7 +30,7 @@ SourceForge. After you acquire the source code, simply use `make` to compile
and copy the single executable `bwa` to the destination you want. The only and copy the single executable `bwa` to the destination you want. The only
dependency required to build BWA is [zlib][14]. dependency required to build BWA is [zlib][14].
###Seeking helps ##Seeking helps
The detailed usage is described in the man page available together with the The detailed usage is described in the man page available together with the
source code. You can use `man ./bwa.1` to view the man page in a terminal. The source code. You can use `man ./bwa.1` to view the man page in a terminal. The
@ -39,7 +39,7 @@ have questions about BWA, you may [sign up the mailing list][6] and then send
the questions to [bio-bwa-help@sourceforge.net][7]. You may also ask questions the questions to [bio-bwa-help@sourceforge.net][7]. You may also ask questions
in forums such as [BioStar][8] and [SEQanswers][9]. in forums such as [BioStar][8] and [SEQanswers][9].
###Citing BWA ##Citing BWA
* Li H. and Durbin R. (2009) Fast and accurate short read alignment with * Li H. and Durbin R. (2009) Fast and accurate short read alignment with
Burrows-Wheeler transform. *Bioinformatics*, **25**, 1754-1760. [PMID: Burrows-Wheeler transform. *Bioinformatics*, **25**, 1754-1760. [PMID:
@ -56,7 +56,7 @@ in forums such as [BioStar][8] and [SEQanswers][9].
Please note that the last reference is a preprint hosted at [arXiv.org][13]. I Please note that the last reference is a preprint hosted at [arXiv.org][13]. I
do not have plan to submit it to a peer-reviewed journal in the near future. do not have plan to submit it to a peer-reviewed journal in the near future.
###Frequently asked questions (FAQs) ##Frequently asked questions (FAQs)
1. [What types of data does BWA work with?](#type) 1. [What types of data does BWA work with?](#type)
2. [Why does a read appear multiple times in the output SAM?](#multihit) 2. [Why does a read appear multiple times in the output SAM?](#multihit)