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?
Hi. GTDB-Tk doesn’t support Euks. GTDB-Tk uses a set of 120 bacterial and 122 archaeal marker genes to place genomes into domain-level trees. Assuming the Euks have a sufficient number of these genes it is possible they will get placed in a basal position. We’ve never tested this case explicitly though.
PhyloRank is a general purpose tool for calculating relative evolutionary divergence. As input, it requires a reference tree so you’d need to put together a multi-domain tree to use if for any sort of domain-level classification task.