Is there a difference in GTDB-taxonomy and metadata between Genbank and Refseq genomes of the same assembly?

GTDB
1

Dear all,

I have a list of different genome assembly accessions for which I want to obtain the GTDB-taxonomy based on the taxonomy files. However, some of my genomes are based on the Genbank format (and it would be difficult for me to change to Refseq) and vice versa. And for the same assembly, GTDB only provides the other version (e.g. "GCA_XYZ instead of “GCF_XYZ”). Also, some of the versions of the genome assemblies are different (e.g. GCF_.1 instead of GCF_.2).

Now, I am wondering whether I can still assign GTDB-taxonomy and metadata (ncbi_isolation_source) to my list of accessions even if they differ in their versions and if they come from Genbank/Refseq.

Thank you very much in advance for your support & I really enjoy the GTDB website by the way!

2

Hi. In the vast (vast!) number of cases this can be done without issue. We have identified a few cases during GTDB curation where different versions of an assembly differ substantially enough to result in a different taxonomic classification. Again, this is very rare.