Scoring representative genomes

GTDB
1

Hi,

Thank you for creating and maintaining such a great resource.

I am interested in dereplicating the full GTDB at different ANI levels. I was hoping to select representatives using the same scoring scheme as described in the documentation here.

Is there a straightforward way to map the column names from the metadata file (*metadata_r214.tsv.gz) to this scoring scheme, or are the scores for each genome in the database available somewhere?

2

Hi,

The scores are not saved anywhere so you would need to recalculate them. You can find a description of each field in this file: https://data.gtdb.ecogenomic.org/releases/latest/auxillary_files/metadata_field_desc.tsv.

I think the mapping should be clear except for maybe determining if a genome is an NCBI representative/reference genome. This is under the ncbi_refseq_category field.

Cheers,
Donovan

3

Thanks very much! I had missed that file.