Does Prokka or gff3 change the sequence / subject ID of fasta files?
Prokka is an annotation tool. It takes your contigs file with fasta headers &gt;NODE_108...and searchs for ORFs and their putative functions. Prokka produces submission ready output, the new fasta headers you see &gt;JHIOGLGG_28...are locus tags and gene description from the annotation and are not related to contig node data. Please see the github information page for more info.