| name | gtdbtk |
| description | Assign bacterial/archaeal taxonomy to MAGs with GTDB. Use this skill when working with gtdbtk: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/Ecogenomics/GTDBTk. For routing across tools, use tool-selection. For end-to-end pipelines, use metagenomics-workflow.
|
| license | MIT |
| category | analysis-tools |
| tags | ["taxonomy","GTDB","MAG"] |
| upstream | https://github.com/Ecogenomics/GTDBTk |
GTDB-Tk
Upstream: Ecogenomics/GTDBTk
Citation
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database. Bioinformatics 38, 5315–5316 (2022). https://doi.org/10.1093/bioinformatics/btac672
See also docs/references.md.
Analytical thinking
GTDB-Tk places genomes into the Genome Taxonomy Database hierarchy (bacterial/
archaeal). Taxonomy is a separate claim layer from binning labels and from
read profilers (MetaPhlAn/Kraken/sylph).
- Pin
GTDBTK_DATA_PATH to a specific GTDB release and cite both GTDB-Tk and
GTDB (gtdb skill).
- Low-quality / chimeric MAGs get misleading placements — filter with CheckM2 +
GUNC first.
- “Novel” high-rank lineages require phylogenetic evidence beyond a single
classify_wf row (trees, redundancy checks, literature).
How to run
export GTDBTK_DATA_PATH=/path/to/gtdb
gtdbtk classify_wf \
--genome_dir drep95/dereplicated_genomes \
--out_dir temp/gtdb_classify \
--extension fa --cpus 16
Optional: gtdbtk infer for trees from MSA outputs.
Related skills
phylogenomics · gtdb · phylophlan · iqtree · drep · checkm2 ·
visualization
