Taxonomy Assignment (bioSkills)

A Claude Code skill that assigns taxonomy to amplicon ASVs/OTUs using classifiers conditioned on the right reference database and primer region, and flags the confidence and over-classification trade-offs.

   
Type Claude Skill
Supplier GPTomics bioSkills (community OSS, MIT)
Availability GA — part of the bioSkills collection
Pricing Free / OSS (MIT) — DADA2, DECIPHER, QIIME2 and the reference databases are separately installed OSS
Capabilities Read/Write — Claude runs the skill’s workflow locally (Bash/R), not as an MCP tool
Verified works · 2026-07-27 — GPTomics/bioSkills resolves; clone + copy install path current
Security cleared · 2026-07-27 — provenance matches GPTomics/bioSkills, MIT, maintained, no OSV advisories

How to install

bioSkills is not an npm package — skills are plain markdown/code read directly by the agent. Clone the repo, then either run the installer for the whole category or copy the single skill directory.

  • Claude Code — clone and install via the bundled script: 
    git clone https://github.com/GPTomics/bioSkills
cd bioSkills
./install-claude.sh --categories "microbiome"

    The installer copies matching skills into ~/.claude/skills/ (default target). Use ./install-claude.sh --list to preview the skills first.

  • Claude Code / other agents — copy just this one skill: 
    cp -r bioSkills/microbiome/taxonomy-assignment ~/.claude/skills/

    (run from inside your clone — the previous step left you in bioSkills/; otherwise replace bioSkills/ with the absolute path of your clone). Install the chosen classifier and reference database when prompted on first use.

What it does

Classifies 16S/ITS/18S ASVs to taxonomy, choosing a classifier and database matched to the amplicon region and desired conservatism:

  • Classifiers — DADA2 assignTaxonomy (RDP 8-mer naive Bayes + bootstrap) + addSpecies (exact 100% match); DECIPHER IDTAXA (tree-descent, novelty-aware, conservative); QIIME2 classify-sklearn (multinomial NB over 7-mers, region-matched training) and classify-consensus-vsearch (global alignment + consensus voting); weighted/clawback classifiers with habitat-specific abundance priors.
  • Reference databases — SILVA (138.1/138.2, 16S), GTDB (r220, genome-based rank-normalized), Greengenes2 (2024.09), UNITE (fungal ITS), PR2 (5.x, protist 18S), and legacy RDP.
  • Guidance — region-specific classifier training, confidence/bootstrap thresholds, and minimizing over-classification.

Primary use cases: taxonomic classification of microbiome ASVs, reference-database selection, confidence-thresholded genus/species calls.

Notes

Distributed as a SKILL.md (plus reference material) in the bioSkills collection — Claude executes the workflow locally rather than as an MCP server. The upstream skill front-matter name is bio-microbiome-taxonomy-assignment; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /taxonomy-assignment. Takes the ASV table produced upstream by amplicon-processing; feeds the microbiome diversity/differential-abundance skills. Upstream directory: microbiome/taxonomy-assignment.

Sources

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