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-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.
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
* Get started
* Smalt documentation
* Smalt repository (binaries/sources)
* bwHPC examples and a moab example script can be found here:
Please read the 'README.bwhpc-examples' file.
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.