When to use --busco_seed_species vs --augustus_species

[mperisin-lallemand]

There have been previous issues posted on understanding the differences between --busco_seed_species and --augustus_species (#251); however, it is unclear to me when to use either parameter. For example, I would like to annotate a Saccharomyces cerevisiae genome. My understanding is that if I use --busco_seed_species saccharomyces_cerevisiae_S288C, then BUSCO will initiate an ORF search using the Augustus saccharomyces_cerevisiae_S288C parameters, run BUSCO, then train Augustus based on the output gene models. If I use --augustus_species saccharomyces_cerevisiae_S288C, then BUSCO will initiate an ORF search with Augustus nidulans parameters, Augustus will then ignore the BUSCO gene models and will use the Augustus saccharomyces_cerevisiae_S288C parameters. Is this correct? Which is the preferred approach for annotating a S. cerevisiae genome?