Interpreting Anvi'o pangenome results

[Libby Brennan]

HI Everyone!

I admit that this is a very loaded question, but I don't know anyone else who has used this program that can help me out so I will be very thankful for any advice!

I recently completed a pangenome analysis using Anvi'o, but frankly just cannot figure out how to analyze the results. I have read the official website as well as a couple others to try and sort it out but I am lost. I know that a lot of it has to do with messing around with the different settings and creating bins, but I am not even sure what to include in different bins. Any advice would be greatly appreciated, or even just pointing me in the direction of a particularly helpful website that gives a good breakdown of it for people who are not well versed in these kinds of analyses. Thank you.

[A. Murat Eren (Meren)]

I think this is a good tutorial that helps people to get better insights into pangenomics is the following:

https://merenlab.org/tutorials/vibrio-jasicida-pangenome/

If you already read that and still don't know how to analyze the results, then perhaps you should consider learning more about pangenomics to contextualize in your mind what questions it can answer (there is a video from our group on YouTube, it may be a good start).

When you have specific questions come to Discord and we will try to help you how to implement them using anvi'o.

Unlike other tools, anvi'o offers a question driven analysis environment. If you are not sure about your questions, then it is not a very useful one :(

Best wishes,

Meren

--
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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