Running RagTag on bacterial short-read assemblies

[ne1al]

Hi! I have short read assemblies from bacterial genomes that I am trying to improve using RagTag. My question is about how I can use RagTag for bacterial genomes considering chromosomal and extrachromosomal genomes (plasmid)? Do you have a tested use case for that? Also plasmid vary much in content. Kindly advise.