I’m going to run a GTDB-Tk on a dataset that has a lot of protists in it in addition to a few bacteria. I was wondering how GTDB-Tk handles bins/MAGs that are eukaryotic such as single-celled algae and diatoms. Would it force a classification into something like a basal archaea or come back as something like NA?
I asked a similar question a while back and you mentioned PhyloRank would be a useful tool in this endeavor. Would you suggest running PhyloRank to get domain level classification, then send all the prokaryotes to GTDB-Tk?