Visualizing SNPs throughout a circular genome

[exo]

Hi there,

I recently sequenced 8 small viral genomes, and when compared to the only publicly available reference more than 250 SNPs were detected. For visualization, i thought it might be a good idea to make the genomes circular and then "plot" the SNPs around every circular genome. Do you know of any program that will be able to do that? I've only used CLC Genomics Workbench for my analysis up to now (sadly im still lacking the bioinformatic skills) and it doesnt support manipulating circular genomes.
It would be nice to visualize if the SNPs actually form a "hot spot".

Your input will be appreciated,
Elias

[Jetse]

Hi Elias,

You can visualize your SNPs with IGV. CLC Genomics Workbench probably produced vcf files, which you can read into IGV . You have to index your vcf files first with igvtools or tabix.
With IGV you can't make your genome circular, but you can show the SNPs of all samples at the same time to search for these hot spots.

[bishwo]

Try Circos. http://www.biostars.org/p/66628/#66642

[LeightonP]

Or Biopython's GenomeDiagram - you can get some quite complex images out of it:



https://twitter.com/pjacock/status/3...865024/photo/1

[exo]

Perfect, thanks for the input!