Roary data visualization with Anvi'o

[JOSE FRANCISCO DELGADO BLAS]

Hi all,

I have previously performed some analysis with Roary and I would like to create a figure with anvi-display-pan including the data form Roary. However, I have tried several times and I am not able to do it.

Could you give me any advice or guideline about the input and the process to get this kind of figure with external data?

Many thanks for your help!

Jose

[A. Murat Eren]

Dear Jose,

I think the best strategy for you is to try to follow this tutorial:

http://merenlab.org/tutorials/interactive-interface/

As you will see, this tutorial takes in an TAB-delimited file that shows the distribution of taxa across metagenomes. You can imagine that the same steps can show you the distribution of gene clusters across genomes. You must be getting an output from Roary that gives you that data.

Of course this wouldn't allow you to do a lot of things you can do with native anvi'o pangenomes. But if you do this and show us that there is promise, we may be able to implement something that imports gene clusters from Roary outputs to do the rest of the workflow natively. I know many people like Roary and we would be happy to modify anvi'o to support Roary so anyone can have access to the best of both workflows.

Best wishes,

--

A. Murat Eren (Meren)
http://merenlab.org :: twitter :: gpg

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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