Can I design a Circos image without an existent genome reference?

Question

[euduca]

Hi, I have three de novo assemblies (with predicted genes and their annotations) of three differents biotypes from a same specie of fungus. There is no reference genome, so I don't know how many chromossomes exists. I found some assemblies from related species, but there is no mention to chromossomes too.

I want to make a visual genomic comparation, so I started to read and study about the Circos.

Is possible to make a visual comparation without a genome reference? I want to demonstrate the difference between the 3 biotypes.

Thanks, Duca.

[Madelaine Gogol]

You have a reference genome, it is your de novo assembly, however draft it may be. It may have lots of scaffolds, but you can use it as if it was a regular genome. You will just have to do some extra work to get it set up with circos.

Answer 1

[mforde84]

Im not entirely sure about circos, but a chord graph in general doesn't need to have a track with a reference assembly. I'm not entirely sure what you have in mind, exactly. A good first step would be to white board the chord graph you want along with what type of relationships you want to represent, then do some investigating to see how to construct it using any number of tools.

[euduca]

Hi.

Thanks for the answer.

The three biotypes are from the same species, so I chose to study a group of genes that are related to virulence factors (effectors) and regions with low similarity ( I want to discover the differences bettween among the biotypes) is interesting too. That's what I have in mind. But, I know I have to study much more, so I asking here to get some directions. I'm blind now.

Regards.