MOB_recon classification of plasmid & chromosome

[mdtorohernando]

Thank you so much for the tool, it’s really useful! I’ve been working with plasmids and their typing through relaxases for many years. Right now, I’m working with high-quality Nanopore assemblies and I’m encountering some classification issues in mob-recon.

I’d like to know what criteria mob-recon uses to classify a contig as a plasmid or chromosome, as I’ve found contigs that are clearly plasmids (based on relaxase and Inc typing, as well as size and MPF system) that have been classified as chromosomes.

In my case, for E. coli, multireplicon IncF plasmids are common, usually with a size greater than 90-100 kb. Many of them in my genomes are classified as chromosomes in mob-recon. We have wet-lab data pointing that there are plasmids.

I would greatly appreciate it if you could explain what leads mob-recon to classify a Nanopore contig as a plasmid or chromosome, as I don’t see the reasoning in this case.

Thanks!

María dT.