How to know that your bacterial genome contain how many plasmids? And which genes are located on which plasmid or chromosome?

Question

[El Niño]

Hi everyone,

I am writing a genome announcement report. Upon reading those written and published previously by other authors, I noticed that they can state exactly which genes are located on which chromosomes and which plasmids. However, when I look at my annotation report, I cannot figure out the locations of some important genes. Can anyone suggest me the software or tools (running on Linux) by which I can run and find such details about the genes in question?

I appreciate all kinds of help.

Best regards,

[Joe]

There isn't really any single tool to do what you want.

It would be helpful to know the organism you're working on, and the quality of your assembly.

Finding plasmids is still difficult, but some things you could do would be to blast your contigs against a known reference for that plasmid (if you have one), inspect the assembly graph for disjoint graph regions, examine contigs you already have for circular permutation (e.g. circlizer IIRC).

You'll likely need to try several things to be confident you've found the plasmids correctly, and even then, there may be sequence missing depending on your assembly quality (e.g. because plasmids often contain repetitive regions etc).