Question: Best tools for circular genome visualization?
2
gravatar for 5heikki
4.9 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

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?

visualization • 8.3k views
ADD COMMENTlink modified 3.5 years ago by Ibrahim Tanyalcin950 • written 4.9 years ago by 5heikki8.4k
10
gravatar for David Fredman
4.9 years ago by
David Fredman990
University of Bergen, Norway
David Fredman990 wrote:

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".

 

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by David Fredman990
4
gravatar for oigl
4.9 years ago by
oigl60
oigl60 wrote:

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 feedbacks are welcome.

ADD COMMENTlink written 4.9 years ago by oigl60
1
gravatar for smithtomsean
4.9 years ago by
smithtomsean170
United Kingdom
smithtomsean170 wrote:

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

ADD COMMENTlink written 4.9 years ago by smithtomsean170
0
gravatar for Ibrahim Tanyalcin
3.5 years ago by
Belgium
Ibrahim Tanyalcin950 wrote:

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/

ADD COMMENTlink written 3.5 years ago by Ibrahim Tanyalcin950
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