Dear developers,
as stated in the instructions, Prokka can skip the Prodigal normal mode if a training file is provided with the --prodigaltf argument. I want to re-annotate some public genomes, and was wondering if I could improve annotation quality by training on all same species complete regfseq genomes. Would pretraining a multifasta with all complete genomes (including plasmids) improve annotation quality ? Is there a considerable cost of speed with this approuch?
My organism of interest has 600 complete genomes in refseq and I have over 3000 to reannotate.
Dear developers, as stated in the instructions, Prokka can skip the Prodigal normal mode if a training file is provided with the --prodigaltf argument. I want to re-annotate some public genomes, and was wondering if I could improve annotation quality by training on all same species complete regfseq genomes. Would pretraining a multifasta with all complete genomes (including plasmids) improve annotation quality ? Is there a considerable cost of speed with this approuch? My organism of interest has 600 complete genomes in refseq and I have over 3000 to reannotate.