Kraken2 Metagenomic Classification (bioSkills)

A Claude Code skill for taxonomic profiling of shotgun metagenomic reads with Kraken2, refined to abundance estimates with Bracken.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT)
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash), not as an MCP tool
Verified	works · 2026-07-20
Security	cleared · 2026-07-20 — provenance matches GPTomics/bioSkills, MIT, skill directory confirmed this run, local Bash workflow wrapping bioconda tools no credentials

How to install

bioSkills is not an npm package — 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 "metagenomics"
```
The installer copies matching skills into ~/.claude/skills/ (default target). Use --list to preview and --dry-run to see what would be copied.
Claude Code / other agents — copy just this one skill:
```
cp -r bioSkills/metagenomics/kraken-classification ~/.claude/skills/
```
(run from inside your clone; otherwise replace bioSkills/ with the absolute path of your clone). Install kraken2, bracken, and KrakenTools (bioconda) plus a reference database when prompted on first use.

What it does

Teaches “who is there” taxonomic profiling of shotgun reads:

Kraken2 — fast k-mer minimizer + lowest-common-ancestor read classification against a chosen reference database.
Bracken — Bayesian rank-level abundance re-estimation to correct read-level misassignments.
KrakenTools / KrakenUniq — unique-minimizer filtering to control false positives.

The skill emphasizes that the database (not the algorithm) determines what can be detected, and draws the critical distinction between read classification, presence detection, and true abundance quantification. Covers database selection/building, confidence-threshold and hit-group tuning, and read-count-to-abundance conversion.

Primary use cases: metagenome taxonomic profiling, reference-database selection, false-positive control, community abundance estimation.

Notes

Distributed as a SKILL.md in the bioSkills collection — Claude executes the workflow locally via Bash rather than as an MCP server. Upstream front-matter name: bio-metagenomics-kraken. Reference databases (e.g., Standard, PlusPF) are large downloads and are not bundled. Complementary to the amr-detection and MetaPhlAn bioSkills metagenomics skills. Upstream directory: metagenomics/kraken-classification.

Sources

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