Genome comparison: Visualization of insertion and deletion

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6.5 years ago

benoit.kunath ▴ 10

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

genome alignment • 1.4k views

ADD COMMENT • link 6.5 years ago by benoit.kunath ▴ 10

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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.

ADD REPLY • link 6.5 years ago by Joe 21k

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

But thanks for the confirmation :)

ADD REPLY • link 6.5 years ago by benoit.kunath ▴ 10

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