| Hilfe-Text | DESCRIPTION
Smalt 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:
* Smalt-backtrack,
* Smalt-SW and
* Smalt-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.
Smalt-MEM and Smalt-SW share similar features such as long-read support
and split alignment, but Smalt-MEM, which is the latest, is generally
recommended for high-quality queries as it is faster and more accurate.
Smalt-MEM also has better performance than Smalt-backtrack for 70-100bp
Illumina reads.
DOCUMENTATION
* Get started
http://www.sanger.ac.uk/science/tools/smalt-0
* Smalt documentation
http://sourceforge.net/projects/smalt/files/smalt_manual.pdf
* Smalt repository (binaries/sources)
http://sourceforge.net/projects/smalt/
* bwHPC examples and a moab example script can be found here:
/opt/bwhpc/common/bio/smalt/0.7.6/bwhpc-examples
Please read the 'README.bwhpc-examples' file.
CITING
SMALT is Copyright (C) 2010 - 2015 Genome Research Ltd.
In case of problems, please contact: bwhpc (at) uni-konstanz.de
This module is available for all users. |