MetaPhlan3-Customizing the database

I have isolated some new species of gut microbes and sequenced their genomes. Now, I want to use Metaphlan3 to study these new bacteria in Metagenomics samples.

I’ve seen tutorials on this: Add the marker sequence stored in a file new_marker.fasta to the marker set: cat new_marker.fasta >> metaphlan_databases/mpa_v31_CHOCOPhlAn_201901_markers.fasta

But I don’t know how to get the marker sequences for the genomes of these new species. What tools or scripts can I use?
Thank you so much for the Metaphlan3 tool! It would be great if it could help me with this problem.

Hi @hhj
Unfortunatelly, we do not have any public script to generate marker genes for a specific species, but you can have a look at the methods section of the Biobakery 3 paper where you can find a deep explanation of the procedure: