The bioBakery help forum

Can markers from CheckM be added to Metaphlan3 database?

Hello,

I’ve been reading about how to extract markers from MAGs (https://groups.google.com/g/metaphlan-users/c/IDU9gAvoilQ/m/nEzbG1mq8WwJ and [BUG] database installation error · Issue #103 · biobakery/MetaPhlAn · GitHub) and still don’t quite understand as I am really a amateur with bioinformatics.

However, I’ve been using CheckM in my MAGs pipeline and wondering if marker genes generated by CheckM can be added directly to MetaPhlan3 database? Do these CheckM markers have the same definition of “marker” as Metaphlan3? or are there any parameter I need to change in CheckM or MetaPhlan when running?

Thank you.
Kitty