Question: Best tools for pan genome analysis?
gravatar for Alec Watanabe
2.2 years ago by
Alec Watanabe60 wrote:

Hi, I'm working with more than a 100 bacterial genomes of Proteus and want to do a pan genome analysis of the genus. I'm currently using Prokka to annotate genomes which were downloaded from the NCBI and Roary will be used for the pan genome analyses. I want to know if:

  1. these softwares are reliable for pan genome analyses;
  2. if they are up-to-date;
  3. if you recommend any other tools for this purpose.

Please, keep in mind that I am working with a significant amount of genomes and thus webtools like PanWeb won't handle this much data.


pan genome tools • 1.8k views
ADD COMMENTlink modified 17 months ago • written 2.2 years ago by Alec Watanabe60

Obligatory link from Omics tools while you wait for other answers.

ADD REPLYlink written 2.2 years ago by genomax92k
gravatar for Joe
2.2 years ago by
United Kingdom
Joe18k wrote:

Roary is written specifically for pangenome analysis, and is designed to take Prokka output

ADD COMMENTlink written 2.2 years ago by Joe18k
gravatar for Alec Watanabe
17 months ago by
Alec Watanabe60 wrote:

Just to update this post for anyone who might come across this post.

I'm currently using GET_HOMOLOGUES for pan genome analysis, but mainly for core genome analysis. The graphical output is good and the software can produce ANI and AAI graphs.

ADD COMMENTlink written 17 months ago by Alec Watanabe60
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