The easy way to get a hierarchical mapping between different taxonomic level

Bacterial Taxonomy
1

Hi,

This is my first time using GTDB (together with Kraken2 and Braken) and I’m looking for a mapping of different taxonomic ids between different different taxonomic level. So example, for the bacterial species Mediterraneibacter faecavium with the tax id 2134035847, I would like to know which genus/family/order it belongs to.

I did find a table called bac120_taxonomy_r207.tsv for the version I’m using, which looks like what I’m looking for. However, the ids in first column there is different from the output ids I got from Braken. As a result, I can’t find 2134035847 in that taxonomy table. Is there an easy way to get such hierarchical mapping somewhere somehow? Thanks in advance.

Kind regards,
Chengyao

2

Hi,

GTDB does not have a native concept of tax ids. However, there are programs such as TaxonKit that can be used to assign tax IDs to GTDB taxa (at all ranks):

Cheers,
Donovan