I recently performed plasmid extraction and nanopore sequencing. I have found what looks like a plasmid with replicon types IncX and IncF. Even with spAdes, canu, unicycler (illumina and nanopore reads), and circlator I am getting the same result.
Do you think this could be a misassembly problem or is possible that this may be a fusion plasmid?
it is entirely possible they fused, such events have been documented in the past (although I don't know about those two specific Inc groups). On the other hand if there is some fairly long repeated elements present on both plasmids then it could be an assembly problem as well. Can you determine whether the predicted size of the molecule from sequence matches up with molecular size from experimental determination?
I am unable to detect their true size prior to sequencing as they are natural plasmids extracted from clinical isolates. I was thinking about doing whole genome sequencing using nanopore to resolve whether it is in fact a fused plasmid
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