ClaudSkills / Science & Research / biology-medicine

bio-metagenomics-metaphlan

Q: What is a Claude Code skill and how does the bio-metagenomics-metaphlan skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-metagenomics-metaphlan is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at https://claudskills.com/learn/what-is-skill-md/.

Category: Science & Research · Sub-category: biology-medicine · Last updated: 2026-06-13

Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads). Covers why a MetaPhlAn percentage is a cell fraction (genome-size-normalized taxonomic abundance) and must never be merged with Kraken/Bracken read fractions, kSGB vs uSGB units for quantifying database-absent taxa, the unknown-fraction rescaling and its version-default flip, --index pinning as a batch variable, and when mOTUs3 or sourmash gather beat marker profiling. Use when profiling who-is-there with high precision, needing HMP-comparable species abundances, quantifying novel taxa, or deciding marker-gene vs k-mer profiling. For k-mer classification see kraken-classification; for strains see strain-tracking; for 16S amplicon see the microbiome category.

About this skill (catalog notes)

bio-metagenomics-metaphlan includes pricing or quota commentary; at least one code block. At roughly 1,934 words the SKILL.md is on the longer end of the catalog distribution.

License: MIT
Original author: GPTomics
Indexed lastmod: 2026-06-13
Catalog position: Science & Research · biology-medicine
Indexed related skills: 10

How bio-metagenomics-metaphlan fits the catalog

bio-metagenomics-metaphlan sits in the Science & Research category under the biology-medicine sub-topic in the ClaudSkills catalog. There are 10 related skills indexed alongside it; comparing a few before installing usually reveals which fits your workflow best.

These notes are auto-generated from features detected in the SKILL.md file and from this catalog's structure — they aren't part of the source repository.

What this skill does

bio-metagenomics-metaphlan is a community-contributed Claude Code skill in the biology-medicine sub-category. It ships as a SKILL.md file that Claude Code auto-discovers under ~/.claude/skills/metaphlan-profiling/ and loads when your prompt matches the skill's trigger.

When to invoke it: Use when profiling who-is-there with high precision, needing HMP-comparable species abundances, quantifying novel taxa, or deciding marker-gene vs k-mer profiling. For k-mer classification see kraken-classification; for strains see strain-tracking; for 16S amplicon see the microbiome category.

Who uses this skill

The bio-metagenomics-metaphlan Claude Code skill is built for researchers, data scientists, academics, and analysts working with complex data and scientific literature. It's part of ClaudSkills (also referred to as Claude Skills or Claude Code Skills) — the open community-curated registry of 116,000+ SKILL.md files for Anthropic's Claude Code agent and the wider Claude ecosystem (Claude API, Claude Agent SDK).

How to install

Free

Manual install (2 steps)

mkdir -p ~/.claude/skills/metaphlan-profiling
curl -L https://claudskills.com/skills/metaphlan-profiling/SKILL.md \
  -o ~/.claude/skills/metaphlan-profiling/SKILL.md

Or just download SKILL.md directly and drop it into ~/.claude/skills/metaphlan-profiling/. Claude Code auto-discovers it on next session.

Skills live at ~/.claude/skills/metaphlan-profiling/SKILL.md on macOS/Linux, or %USERPROFILE%\.claude\skills\metaphlan-profiling\SKILL.md on Windows. See the full install guide for step-by-step instructions.

📱 Install from your phone or desktop Telegram

Open @claudskills_bot on Telegram, tap Open Desktop App, and the desktop app installs this skill for you. Or share the bot link with a colleague — they get the same one-tap install. Learn more →

Pro

One-click install via the desktop app

The ClaudSkills desktop app installs any skill directly into ~/.claude/skills/ with one click — no terminal required. Pro starts at $9/mo or $149 lifetime.

Pro

For the full experience including quality scoring and one-click install features for each skill — upgrade to Pro.

See pricing → Download desktop app

Frequently asked questions

How do I install the bio-metagenomics-metaphlan Claude Code skill?

Install via the ClaudSkills desktop app (one click) or copy SKILL.md from the source repository to ~/.claude/skills/metaphlan-profiling/SKILL.md and restart Claude Code. Both flows are detailed at claudskills.com/install/.

What does the bio-metagenomics-metaphlan skill do?

Is this skill free to install?

Yes. ClaudSkills is an open registry — every skill keeps its source repository's license, and manual install via copy is free. ClaudSkills Pro ($9/mo, $79/yr, or $149 one-time) adds one-click install via the desktop app and a multi-signal Quality Score.

When should I use the bio-metagenomics-metaphlan skill?

Use bio-metagenomics-metaphlan when your Claude Code task falls under the Science & Research category — specifically in the biology medicine area. Claude Code auto-discovers installed skills and invokes the right one based on the task description, so you can also ask Claude directly (e.g. "use bio-metagenomics-metaphlan" or describe the task and let Claude pick). Browse related skills at /category/science/.

What is a Claude Code skill and how does the bio-metagenomics-metaphlan skill fit in?

A Claude Code skill is a SKILL.md file that lives under ~/.claude/skills/<name>/ and tells the Claude Code CLI agent how to perform a specific task (instructions, prompts, allowed tools). Skills are auto-discovered at session start. bio-metagenomics-metaphlan is one of 67,000+ skills indexed in the open ClaudSkills catalog, classified under the Science & Research category. Learn more at /learn/what-is-a-claude-skill/.

Attribution & license

Source: https://github.com/GPTomics/bioSkills/blob/b4c135522044863f2225d50772c596e603cb7100/metagenomics/metaphlan-profiling/SKILL.md
License: MIT
Author: GPTomics

Cite this skill

If you reference this skill in a blog post, paper, or documentation, you can cite it as:

APA

GPTomics. (2026). bio-metagenomics-metaphlan [Claude Code skill]. ClaudSkills. https://claudskills.com/skills/metaphlan-profiling/

BibTeX

@misc{metaphlan-profiling-2026,
  author    = {GPTomics},
  title     = {bio-metagenomics-metaphlan [Claude Code skill]},
  year      = {2026},
  publisher = {ClaudSkills},
  url       = {https://claudskills.com/skills/metaphlan-profiling/}
}

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Badge

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