Difference between revisions of "Augustus"
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Since the directory where Augustus is installed is not user-writable make a copy of the Augustus config and set the '<code>$AUGUSTUS_CONFIG_PATH</code>' variable to the new path e.g. | Since the directory where Augustus is installed is not user-writable make a copy of the Augustus config and set the '<code>$AUGUSTUS_CONFIG_PATH</code>' variable to the new path e.g. | ||
rsync -a $HPC_AUGUSTUS_CONF . | rsync -a $HPC_AUGUSTUS_CONF . | ||
| − | export AUGUSTUS_CONFIG_PATH=/ufrc/group/user/some/project/augustus_conf_dir | + | export AUGUSTUS_CONFIG_PATH=/ufrc/group/user/some/project/augustus_conf_dir/config |
in the job script before running Augustus or [[Busco]]. | in the job script before running Augustus or [[Busco]]. | ||
Revision as of 21:46, 27 July 2020
Description
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server or be downloaded and run locally. AUGUSTUS usually belongs to the most accurate programs for the species it is trained for. Often it is the most accurate ab initio program. AUGUSTUS can predict alternative splicing and alternative transcripts. AUGUSTUS can predict the 5'UTR and 3'UTR including introns. AUGUSTUS is retrainable. It comes with a training program that estimates the parameters given a training set of known genes. It also comes with an optimization script that tries to find values for the meta parameters, like splice window sizes, that optimize the prediction accuracy. AUGUSTUS can be used ab initio and has a flexible mechanism for incorporating extrinsic information, e.g. from EST alignments and protein alignments.
Required Modules
Serial
- augustus
System Variables
- HPC_AUGUSTUS_DIR - installation directory
Additional Information
Since the directory where Augustus is installed is not user-writable make a copy of the Augustus config and set the '$AUGUSTUS_CONFIG_PATH' variable to the new path e.g.
rsync -a $HPC_AUGUSTUS_CONF . export AUGUSTUS_CONFIG_PATH=/ufrc/group/user/some/project/augustus_conf_dir/config
in the job script before running Augustus or Busco.