structural variants from mauve

Question

[rthapa]

Hi,I am doing de novo assembly of a bacterial genome from nanopore sequence reads with canu. I wanted to see the structural variants in the assembled genome compared with reference genome. I see some structural variants using mauve. I wonder if there is any way to detect if they are the real variants or due to error in the assembly. I see many inversions so I doubt if they are the real inversions. I would appreciate any suggestion. Thanks

[samuel.a.odonnell]

One possibility would be to generate multiple genome assemblies (considering it is a single bacterial genome it shouldn't take so long and many are much faster than canu) and see if they all contain the same rearrangements. To check all the genomes for similar rearrangements you could use a tool like MUM&Co and then look the overlaps between assemblies.

Read alignment is another option to check the arrangement. However inversions generally occur within repeated elements so manually looking at the alignment would be difficult as it will most likely be a complicated region. So you could try a tools like cuteSV to detect the variants using the read alignment and see if they are the same.