This got closed before I could respond -
I was looking for a tool that could convert the SGB profile table into GTDB taxonomy? Is the only way to get GTDB taxonomy by using fasta files as input?
Hi @bethp
Whoops! But glad you came back into a new topic since this a good question to have in a distinct place.
Currently, the options are:
- At all of the UseGalaxy servers
- GTDB-Tk Classify genomes by placement in GTDB reference tree
- This uses a fasta query, and it is expected to be an assembly
- In addition, at the UseGalaxy.eu server
- NCBI-GTDB map Map taxonomic classifications between the NCBI and GTDB taxonomies
- Tabular file with either NCBI taxonomic names or GTDB taxonomic names, to convert to the other system.
I haven’t used that second tool yet (some of these tools are new and under active development!) but it seems like if you can get your data process up through NCBI taxonomic names from any other method, and obtain the mapping file, then this should work. But let us know if you run into problems and we can troubleshoot with a (small please) example you share. 