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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
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 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
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,
**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
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
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
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
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
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
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)
2. [Why does a read appear multiple times in the output SAM?](#multihit)