Detecting structural variants when comparing assembled genome and reference

Question

[godeludanu]

I have a bacterial genome which has been assembled de novo from nanopore reads. I wish to compare this with a reference to detect all structural variants (this is an exploratory study, we do not currently have specific variations in mind).

Is there a single pipeline / tool to achieve what I am looking for?

Answer 1

[skbrimer]

You might try Sybil http://sybil.sourceforge.net/ I have not used it without someone holding my hand in a training seesion, but it had a really cool synteny gradient view that would should rearrangements pretty easily.