Augustus

Description

AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke, Oliver Keller, Stefanie König, Lizzy Gerischer and Katharina Hoff. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and syntenic genomic alignments. Since version 3.0 AUGUSTUS can also predict the genes simultaneously in several aligned genomes.

License

Artistic Licence

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of augustus and load default version of augustus as

module avail augustus/ # list available modules
module load augustus   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail augustus

and choose explicit version you want to use.

You may need to adjust environment variable AUGUSTUS_CONFIG_PATH to point to some writable directory with configurations. Eg.:

mkdir $SCRATCHDIR/augustus_configs
cp -r $AUGUSTUS_CONFIG_PATH/* $SCRATCHDIR/augustus_configs/
export AUGUSTUS_CONFIG_PATH=$SCRATCHDIR/augustus_configs

Documentation

https://github.com/Gaius-Augustus/Augustus/blob/master/README.TXT or in directory /software/augustus/3.3.1/src

Homepage

http://bioinf.uni-greifswald.de/augustus/
https://github.com/Gaius-Augustus/Augustus