MetaPhlAn Profiling (bioSkills)

A Claude Code skill that profiles shotgun metagenomes to species and species-level genome bin (SGB) abundance using MetaPhlAn 4’s clade-specific marker genes, and keeps the resulting units interpretable.


Type	Claude Skill
Supplier	GPTomics bioSkills (community OSS, MIT)
Availability	GA — part of the bioSkills collection
Pricing	Free / OSS (MIT) — MetaPhlAn, Bowtie2, minimap2 and the marker database are separately installed OSS
Capabilities	Read/Write — Claude runs the skill’s workflow locally (Bash/Python), not as an MCP tool
Verified	works · 2026-08-03
Security	cleared · 2026-08-03 — GPTomics/bioSkills MIT confirmed, provenance matches, no 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 "metagenomics"
```
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/metagenomics/metaphlan-profiling ~/.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 MetaPhlAn and download the marker index when prompted on first use.

What it does

Runs marker-gene taxonomic profiling and explains the units it produces:

Workflow — align reads to clade-specific markers (Bowtie2 for short reads, minimap2 for long reads), detect clades whose private markers are present, average per-marker coverage with a quantile-truncated robust mean (--stat_q), normalize to genome-size-aware cell fractions, optionally estimate the database-absent UNCLASSIFIED fraction, and re-profile cached mappings at other taxonomic levels.
Unit discipline — a MetaPhlAn percentage is a genome-size-normalized cell fraction and must not be pooled with Kraken/Bracken read fractions; covers kSGB vs uSGB units for quantifying taxa absent from the database, the unknown-fraction rescaling and its version-default flip, and pinning --index because the database version is a batch variable.
Alternatives — when mOTUs3 or sourmash gather are the better choice than marker profiling.
Components — MetaPhlAn 4.1+ (~189 markers per SGB), Bowtie2 2.5.3+, minimap2 2.26+, pandas 2.2+, and the mpa_vJun23_CHOCOPhlAnSGB index family.

Primary use cases: species/SGB relative abundance from shotgun metagenomes, cross-study profile harmonization, long-read metagenome profiling.

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-metagenomics-metaphlan; if invoked as a namespaced plugin command it resolves under the bioSkills plugin, not as a bare /metaphlan-profiling. Complements the catalogued Kraken Classification skill, which produces read-fraction profiles from the same input — the skill is explicit that the two abundance types are not interchangeable. Feeds the strain-tracking and functional-profiling skills. Upstream directory: metagenomics/metaphlan-profiling.

Sources

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