These scripts run all the steps needed to:
- Quality trim and filter transcriptome reads with trim_galore,
- Identify repeats in your genome de novo with RepeatModeler,
- Mask repeats with RepeatMasker,
- Run ProtHint to generate hints from translated transcriptomes (or do this as part of the BRAKER3 pipeline),
- Map trimmed/filtered reads to the genome with STAR/HISAT2,
- Run BRAKER to annotate the genome
Some relevant reading: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ http://www.repeatmasker.org/RepeatModeler/ http://www.repeatmasker.org/RepeatMasker/ https://www.biostars.org/p/411101/ https://github.com/gatech-genemark/ProtHint https://github.com/Gaius-Augustus/BRAKER/ https://github.com/Gaius-Augustus/TSEBRA
Note that these scripts are written for Kevin Kocot's workstation and some paths are hard-coded (search for "wirenia" to find them)