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.