How can I analyze and compare the core genome of several organisms?

Question

[Airam]

Hello

I'm new at bioinformatics, so sorry for my possible mistakes. I'm trying to analyze and compare the core-genome of several microorganisms, but I don't know any suitable software. I tried the new PGAP-X, that is something similar of what I need, but I can't retrieve *.ptt files necessary for the program working because NCBI has replaced them for the "feature_table" different format. I've tried to change the extension format, but it didn't work.

Anyone can help me? I've tried with others like Mauve or Harvest, but I don't know if it could exists something more specific. Roary, Get_Homologues and BPGA are other core-analyzer tools that could work, but maybe I'm searching for something simpler.

Thank you

Answer 1

[Carambakaracho]

Maybe Busco or CheckM are what you need? Both programs are designed to check for genome completeness - based on precomputed models.