gtdbtk

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