Genome comparison: Visualization of insertion and deletion

Question

[benoit.kunath]

Hello,

I try to generate figure to show difference between my microbial genomes (different strains). So far, I only found software that use reference genome and map the others genomes against that reference. However, that systems only allow me to see things that are missing in my strains or that are not identical to the reference (like with BRIG for example).

It's there a software out there where I can give a reference genome + several strains as query and that will give me some ring picture where I can see both insertion and deletion??

Thanks a lot for your help, Best,

Ben

[Joe]

You could try Circos, but people generally hate circos plots because they don’t really show much very clearly. Especially if you are looking for small INDELs in large sequences.

[benoit.kunath]

Yes that's the software I always find but it seems extremely complicated to learn...

But thanks for the confirmation :)