I am attempting to assemble a part of a prokaryotic genome from an illumina assembly of a prokaryotic cell. We were advised to generate our own matrix file with gmsn.pl using our assembled genome. Previously to this we assembled the genome with velveth and velvetg. My question is - for gmsn.pl matrix creation, do I use the contigs.fa or the Sequences file in the velvetg output? All they say about gmsn.pl in the GeneMark manual is to us the assembled genome and not much more in regards to that. Thanks!