Burrows Weeler Aligner (BWA) is a software package for mapping
low-divergent sequences against a large reference genome, such as
the human genome.
It has two major components, one for read shorter than 150bp
and the other for longer reads.
It consists of three algorithms:
* BWA-SW and
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 long-read support
and split 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
SAMtools is a popular open-source tool used in next-generation sequence
analysis. This primer provides an introduction to SAMtools, and is geared
towards those new to next-generation sequence analysis. The primer is
also designed to be self-contained and hands-on, meaning that you only
need to install SAMtools, and no other tools, and sample data sets are
* BWA: get started and FAQs
Read the /opt/bwhpc/common/bio/bwa/0.7.12/README.md file
For BWA command line options enter: bwa (exit-status 1).
* SAMTOOLS: Home and tutorial
* BWA manual page
* BWA repository (binaries/sources)
* bwHPC examples and a moab example script can be found here:
Please read the 'README.bwhpc-examples' file.
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)
MPI is not supported by BWA.
There is a pBWA (Parallel BWA) version available.
Some tools are able to run multithreaded (-t threads).
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users.