I am doing a pan- / coregenome study comparing different strains of the same bacterial species.
Would you exclude the plasmids from this comparison? If yes/no: what is your reasoning?
I know, this depends on the question and on the type of plasmids. What I can say is that the plasmids are quite small (lower 50kb in general). Also, it might be that some plasmids for some strains are missing.
Or is there a "best practice"? (maybe review or so?)