Hi.. I made my peace with GGBs and SGBs. Thank you so much for this. You helped me with one of the major issues I was facing, mentioned in this post. Make custom metaphlan database by adding some more genomes
I am undertaking this project with minimal experience in database building processes. So, the Metaphlan GitHub page does not mention anything about making SGB-specific marker sets, except for the explanation given in the main paper methodology. My question is, while defining the markers for an SGB, what identity and coverage should I consider to eliminate gene sequences already present in the Metaphlan marker database?