The NCBI Taxonomy Database

For some parts of the annotation format, DENOFO needs access to the NCBI Taxonomy Database through the ete3 library. When you first run a tool that needs the NCBI Taxonomy Database (e.g., denofo-questionnaire) and the database could not be found, it will download and process it, which can take some minutes. This local database version will be used from now on without additional waiting times.

In case you want to update your local version of the NCBI Taxonomy Database, please run:

update-ncbi-taxdb
# or for uv
uv run update-ncbi-taxdb