How to detect which plasmids occur multiple times in a collection of fragmented whole genome assemblies?

Question

[bas1993]

I have whole genome assemblies of >100 bacterial isolates that are very fragmented (short read sequencing, MiSeq). In this dataset I determined that there are various plasmids present with PlasmidFinder. I want to do long read sequencing on a small selection within this collection, but I want to try to sequence as much unique plasmids as possible. Therefore I want to determine which isolates contain reoccurring plasmids in this collection.

So I tried to manually BLAST 1 contig of 1 isolate with a plasmid replicon to all isolates with the options to only show hits >90% identity and >90% coverage. However, this results in some false negatives if the plasmid is more fragmented in another isolate.

Does anyone have tips how to adjust BLAST settings (or maybe another tool) and how to do this more efficiently?

And does anyone know how to quickly extract all contigs that have a PlasmidFinder hit?

Answer 1

[hugo.avila]

Hi, some time ago i read this paper: https://mbio.asm.org/content/11/1/e03284-19. They did exactly what you want to do. I hope this helps ;)