Based on the lack of information from fragmented genomes, where there is not a correct description if the contig belongs to the bacterial chromosome or it comes from a plasmid, one option is to perform a BLASTn against the complete genomes from plasmids. It may limit the results to the information already available in public databases without the possibility to detect new plasmids or plasmids which acquired new genes. Do you know any too available to help to solve this problem?

Avoiding VecScreen, please.