AUGUSTUS

Augustus is available on Karle, users must load the module by typing:

module load augustus/[current-version]

The current version can be found in /share/usr/augustus. More detailed information about AUGUSTUS capabilities along with data sets can be found on AUGUSTUS web page:

http://bioinf.uni-greifswald.de/augustus/

When used in research the AUGUSTUS must be cited with appropriate paper from the following list:

Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack (2011)
A novel hybrid gene prediction method employing protein multiple sequence alignments
Bioinformatics, doi: 10.1093/bioinformatics/btr010
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008)
Using native and syntenically mapped cDNA alignments to improve de novo gene finding
Bioinformatics, 24(5), pages 637-644, doi: 10.1093/bioinformatics/btn013
Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006)
"AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome"
BMC Genome Biology, 7(Suppl 1):S11.
M. Stanke , O. Schöffmann , B. Morgenstern, S. Waack (2006)
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources 
BMC Bioinformatics 7, 62.
Mario Stanke and Burkhard Morgenstern (2005)
"AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints",
Nucleic Acids Research, 33, W465-W467
Mario Stanke, Rasmus Steinkamp, Stephan Waack and Burkhard Morgenstern (2004) 
"AUGUSTUS: a web server for gene finding in eukaryotes" 
Nucleic Acids Research, Vol. 32, W309-W312
Mario Stanke and Stephan Waack (2003)
Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. 
Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225
Mario Stanke (2003)
Gene Prediction with a Hidden-Markov Model. 
Ph.D. thesis, Universität Göttingen

AUGUSTUS is sequential program Thus the following basic script can be used to run workflow with AUGUSTUS:

#!/bin/bash
#SBATCH --partition production
#SBATCH --job-name my program
#SBATCH --nodes=1
#SBATCH --ntasks=1

cd SLURM_SUBMIT_DIR

augustus <input_file>  > <output_file>