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Best tools for pan genome analysis?

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.

Thanks!

pan-genome
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updated by Ram Ram • written by Alec Watanabe Alec Watanabe

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

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written by GenoMax GenoMax

2 answers

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

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written by Joe Joe

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.

• 0 views • link
written by Alec Watanabe Alec Watanabe

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