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:
- these softwares are reliable for pan genome analyses;
- if they are up-to-date;
- 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.