From d67e9230269f4ef447878b0c28ea1480091afc6f Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 14 May 2014 14:33:42 -0400 Subject: [PATCH] changed the heading format --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 0835721..78bc150 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -###Getting started +##Getting started git clone https://github.com/lh3/bwa.git cd bwa; make @@ -6,7 +6,7 @@ ./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)