| name | gtdb |
| description | Use the Genome Taxonomy Database (GTDB) public releases — taxonomy tables, trees, metadata, and representative genomes. Use this skill when: (1) Choosing or citing a GTDB release, (2) Downloading bac120/ar53 taxonomy or reps, (3) Distinguishing GTDB data files from the GTDB-Tk runtime package, (4) Preparing reference sets for MAG comparison. Upstream: https://gtdb.ecogenomic.org/ and https://github.com/Ecogenomics/GTDBTk. For classifying your MAGs, use gtdbtk. For biome catalogues, use mgnify. For routing, use public-databases.
|
| license | MIT |
| category | utilities |
| tags | ["database","GTDB","taxonomy","genomes"] |
| upstream | https://gtdb.ecogenomic.org/ |
GTDB (Genome Taxonomy Database)
Portal: https://gtdb.ecogenomic.org/ ·
Downloads: https://gtdb.ecogenomic.org/downloads ·
Data: https://data.gtdb.ecogenomic.org/releases/ ·
Toolkit: Ecogenomics/GTDBTk
Citation
Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol. 38, 1079–1086 (2020). https://doi.org/10.1038/s41587-020-0501-8
Parks, D. H. et al. GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes. Nucleic Acids Res. 54, D743–D754 (2026). https://doi.org/10.1093/nar/gkaf1040
See also docs/references.md.
Analytical thinking
GTDB provides a rank-normalized prokaryotic taxonomy. Your MAG labels from
binning are not taxonomy — GTDB assignment is a separate claim layer.
Distinguish three packages people confuse:
| Package | What it is | Typical use |
|---|
GTDB release files (bac120_taxonomy.tsv, trees, metadata, genome reps) | Public taxonomy/genome release | Cite taxonomy; build custom refs |
GTDBTK_DATA_PATH / gtdbtk_data.tar.gz | Runtime DB for GTDB-Tk | Classify genomes with gtdbtk |
| MGnify biome catalogues | Biome MAG catalogues (often GTDB-annotated) | Novelty / habitat context (mgnify) |
Always pin the GTDB release ID (e.g. R10-RS226 from VERSION.txt / release notes) next to GTDB-Tk software version.
GTDB release 10 (R10-RS226) notes
From Parks et al. (Nucleic Acids Res. 2026):
- ~715k bacterial + ~17k archaeal genomes; ~137k bacterial / ~7k archaeal species clusters
- Major new deep lineages are rarer each release (diversity saturation signal), but species discovery continues (>95% species still ungenomed under their projections) — do not claim “GTDB is complete”
- Website / ANI methodology updates (e.g. skani in recent releases) — match GTDB-Tk data package to the release you cite
- Prefer
releases/<release>/ over assuming latest/ stays frozen mid-study
Prerequisites
| Need | Resource |
|---|
| Taxonomy tables / trees | https://data.gtdb.ecogenomic.org/releases/latest/ |
| Representative genomes | genomic_files_reps/ (very large) |
| Classify MAGs | GTDB-Tk data package → gtdbtk skill |
How to fetch release metadata
mkdir -p db/gtdb && cd db/gtdb
wget -c https://data.gtdb.ecogenomic.org/releases/latest/VERSION.txt
wget -c https://data.gtdb.ecogenomic.org/releases/latest/RELEASE_NOTES.txt
wget -c https://data.gtdb.ecogenomic.org/releases/latest/bac120_taxonomy.tsv.gz
wget -c https://data.gtdb.ecogenomic.org/releases/latest/ar53_taxonomy.tsv.gz
For GTDB-Tk classification DB, follow the official GTDB-Tk data install docs
(not ad-hoc genome tarballs) — see gtdbtk skill.
Key files (thinking)
| File | Use |
|---|
bac120_taxonomy.tsv / ar53_taxonomy.tsv | Map genome → GTDB lineage |
*_metadata.tsv.gz | Quality / NCBI cross-refs / stats |
bac120.tree / ar53.tree | Reference phylogeny |
genomic_files_reps/ | Species-rep FASTA/proteins (huge) |
Decision tree
GTDB-related task?
├─ Classify my MAGs → gtdbtk (needs GTDB-Tk data package)
├─ Cite / parse taxonomy release tables → gtdb (this skill)
├─ Compare to human-gut species catalogue → mgnify (UHGG) ± gtdb labels
└─ Read-based species tables only → metaphlan / kraken2 (not GTDB placement)
Related skills
gtdbtk · public-databases · mgnify · progenomes · cami · checkm2 · drep · mag-qc · visualization
