This is a collection of scripts to perform the training of TwinScan/SNAP/Augustus/GeneID.

Required:

augustus (set AUGUSTUS_CONFIG_PATH accordingly)

N-scan and IPE (http://mblab.wustl.edu/software.html)

EVAL (http://mblab.wustl.edu/software.html; set the parameter "EVAL_GTF" to point to the directory containing its scripts)

gtf2gff3 (http://www.sequenceontology.org/software/GAL_Code/GAL_0.2.2_stand_alone_scripts.tar.gz)

As input, prepare_dataset.py takes the proteins, the GTF, and the masked and unmasked genome. The GTF must contain the start/stop codon features; they can be added with refeature from PHAST (http://compgen.cshl.edu/phast/index.php).