I have been finding the Prokka software to be very useful annotating an assembled bacterial genome (contigs). I wanted to know if anyone has recommendations on how to determine if the assembled bacterial genome (contigs) contains a plasmid. If so, how many plasmids and length of plasmids.
I tried using PLSDB and PlasmidFinder with a bacteria genome I downloaded that reportedly has one plasmid - and both software returned no hits. I also ran these software on my assembled bacterial genome and received no hits (although I am not too confident in this result given that they returned no hits for the known downloaded bacterial genome, and it could be because I am not using them correctly).
My output from Prokka does not seem to contain information about presence/absence of plasmids and it seems it may not be designed to find plasmids. Any advice on an elegant solution to find plasmids in the assembled contigs (I do not want to do something too manual like blast each contig individually - because I plan to repeat the procedure for many assembled genomes)?