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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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Using viridiplantae database directly #712

Closed ardy20 closed 10 months ago

ardy20 commented 10 months ago

Hi Can we directly use a downloaded Viridiplantae database in --prot_seq=proteins.fa option?

We downloaded it from OrthoDB 11: https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11/ Regards

KatharinaHoff commented 10 months ago

Yes, you can. You can consider simplifying the FASTA headers with https://github.com/Gaius-Augustus/Augustus/blob/master/scripts/simplifyFastaHeaders.pl (BRAKER may complain about the whitespaces in the headers, it's not killing the pipeline though).