git clone https://github.com/lh3/bwa.git cd bwa; make ./bwa index ref.fa ./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 is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It 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 the support of long reads and chimeric 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.
For all the algorithms, BWA first needs to construct the FM-index for the 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.
BWA is released under GPLv3. The latest souce code is freely
available at github. Released packages can be downloaded at
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 of BWA is zlib.
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
HTML version of the man page can be found at the BWA website. If you
have questions about BWA, you may sign up the mailing list and then send
the questions to firstname.lastname@example.org. You may also ask questions
in forums such as BioStar and SEQanswers.
Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. [PMID: 19451168]. (if you use the BWA-backtrack algorithm)
Li H. and Durbin R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595. [PMID: 20080505]. (if you use the BWA-SW algorithm)
Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]. (if you use the BWA-MEM algorithm or the fastmap command, or want to cite the whole BWA package)
Please note that the last reference is a preprint hosted at arXiv.org. I do not have plan to submit it to a peer-reviewed journal in the near future.