I have been using this pipeline for prokaryotes and it works great. I have a dataset with quite a bit of marine protists, is there any support or planned support for protists? I found MMETSP (https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001889) and I’m wondering if it’s possible to format this to include with the existing version 95 of GTDB-tk?
We have and continue to explore extending the GTDB to other groups, but there are no immediate plans to do this. Funding and available resources are a limiting factor. You can look at PhyloRank (https://github.com/dparks1134/PhyloRank) if you wish to create an RED scaled protist tree. As you might imagine, it is a fair effort to then curate this tree to follow the criteria used by the GTDB. Sorry we can’t be of direct help.
Thanks for getting back to me so quickly. I’ll absolutely use PhyloRank in the future. Hopefully your team will get additional funding in the future to address the protist problem. Though, the problem is more upstream of GTDB-Tk anyways as many of the metagenomic binners use bacterial and/or archaeal markers (e.g. MaxBin2) and, I believe, DAS_Tool’s single copy genes are prokaryotic as well.