Best tools for pan genome analysis?
2
0
Entering edit mode
2.8 years ago

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 tools • 2.4k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode
2.8 years ago
Joe 19k

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

ADD COMMENT
1
Entering edit mode
2.1 years ago

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 COMMENT

Login before adding your answer.

Traffic: 1871 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6