Best tools for circular genome visualization?

Question

[5heikki]

What do biostars use for circular-mapping genome visualization? DNA plotter, which comes with Artemis, is quite basic and doesn't IMO produce publication grade figures. In the past, I have used highly configurable Circos for one publication and I think it's still quite popular. I was just wondering, what else is out there?

Answer 1

[David Fredman]

I think Circos may still be the most powerful option for circular plots (but keen to hear about alternatives, too).

There's the RCircos package in bioconductor if you prefer that way of providing parameters

You might find hive plots an interesting alternative for some applications. Tools to create them include the jhive java implementation and others listed on the hiveplots.net site under "Hive plot code and applications".

Answer 2

[oigl]

Hi! I'm from UGENE team. We have a simple Circular View, but it produces nice images, so I thought, you might like to try it.

Note that we're going to improve Circular View in the program future versions. Any feedback is welcome.

Answer 3

[smithtomsean]

From what I understand, Circos still produces the best quality figures for publication. ggbio is an alternative built on Bioconductor GRanges objects and ggplot.

Answer 4

[Ibrahim Tanyalcin]

Here is an interactive version of circos designed for protein sequence data. It can be simultaneously used for live presentations and/or publication quality figures:

http://i-pv.org/