Visual Representation Of Multiple Genomes?

Question

[peris]

Hi All

Firstly wish you all a very happy new year 2014. I have done whole genome sequencing of 10 member of a family and called structural variants (SNV, InDels, translocations) on them. Now I want to represents all these structural variants in one image. I know there is tool "circos" which is very nice; but for multiple genome I am hesitating to use it. Can the community members suggest me some tool for representing all the 10 genomes in one image?

Answer 1

[Charles Warden]

I think POMO provides exactly the functionality that you are looking for (and I find it much easier to use than circos for individual genome plots anyways):

http://www.biomedcentral.com/1471-2164/14/918/abstract

http://pomo.cs.tut.fi/

I recommend using Firefox - I've encountered bug to two with Google Chrome (and it doesn't work at all with IE)

Answer 2

[Pavel Senin]

We just worked out some simple R-based plots Visualization Of Cnv With Genomic Coordinates In R Ggplot2 Or Ggbio. It is fairly simple to add additional columns and color groups to each of the samples corresponding to your features.