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Agent skill

Bio Microbiome Qiime2 Workflow

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

QIIME2 command-line workflow for 16S/ITS amplicon analysis. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

No licenceAuto-check passed

Install Bio Microbiome Qiime2 Workflow

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-qiime2-workflow --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-microbiome-qiime2-workflow .claude/skills/bio-microbiome-qiime2-workflow && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
bio-microbiome-qiime2-workflow
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.6k tokens
SKILL.md length
179 words
Files
3
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

QIIME2 command-line workflow for 16S/ITS amplicon analysis. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.

  • Preferring CLI over R
  • SKILL.md covers Version Compatibility, Import Data, Denoise with DADA2 and Alternative: Deblur Denoising, plus 8 more sections
  • Runs Shell scripts from its folder; reaches data.qiime2.org
  • Needing reproducible provenance

What it does

Bio Microbiome Qiime2 Workflow is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/qiime2_16s.sh` and `usage-guide.md`).

The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Preferring CLI over R
  • Needing reproducible provenance
  • Working within QIIME2 ecosystem

Example prompts

  • “/bio-microbiome-qiime2-workflow”

Requirements

  • Python 3
  • A Bash shell

What it can do on your machine

Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships script files (Shell), which the agent can run.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • data.qiime2.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Microbiome Qiime2 Workflow loads about 1.6k tokens when it runs. Until then it costs about 67 tokens; SKILL.md has 179 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~67
When it runs · the whole SKILL.md, loaded when a task matches
~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

Without a licence we can't republish the file, so here is its outline and opening line. It has 179 words (~1,555 tokens).

“Reference examples tested with: DADA2 1.30+, MAFFT 7.520+, QIIME2 2024.2+, phyloseq 1.46+, scanpy 1.10+, scikit-learn 1.4+”

— opening of SKILL.md by FreedomIntelligence
name
bio-microbiome-qiime2-workflow
tool_type
cli
primary_tool
qiime2

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-microbiome-qiime2-workflow of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/qiime2_16s.sh
  • usage-guide.md

Open the folder on GitHubat commit b1f9b6e

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Bio Microbiome Qiime2 Workflow next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Bio Microbiome Qiime2 Workflow compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Microbiome Qiime2 Workflow this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.6kAutomated safety check: PassNone
Qiime2 AmpliconK-Dense-AI/scientific-agent-skills48k1 repos~2.2kAutomated safety check: PassMIT
Bio Microbiome Amplicon ProcessingGPTomics/bioSkills1.2k1 repos~5.7kAutomated safety check: PassMIT
Bio Microbiome Qiime2 WorkflowGPTomics/bioSkills1.2k1 repos~5.7kAutomated safety check: PassMIT
Waypoint BioK-Dense-AI/scientific-agent-skills48k1 repos~4.2kAutomated safety check: PassMIT
Bio Workflows Microbiome PipelineGPTomics/bioSkills1.2k1 repos~6.1kAutomated safety check: PassMIT

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Questions about Bio Microbiome Qiime2 Workflow

What does Bio Microbiome Qiime2 Workflow do?

QIIME2 command-line workflow for 16S/ITS amplicon analysis. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bio Microbiome Qiime2 Workflow is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. QIIME2 command-line workflow for 16S/ITS amplicon analysis.

When should I use Bio Microbiome Qiime2 Workflow?

Bio Microbiome Qiime2 Workflow fits situations like: preferring CLI over R; needing reproducible provenance; working within QIIME2 ecosystem.

How do I install Bio Microbiome Qiime2 Workflow in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow -a claude-code`. Or copy the skill folder (skills/bio-microbiome-qiime2-workflow in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-microbiome-qiime2-workflow in your project. Claude Code loads it when a task matches its description.

How do I install Bio Microbiome Qiime2 Workflow in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow -a codex`. Or copy the skill folder (skills/bio-microbiome-qiime2-workflow in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-microbiome-qiime2-workflow in your project. Codex loads it when a task matches its description.

Can I use Bio Microbiome Qiime2 Workflow in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-qiime2-workflow -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-microbiome-qiime2-workflow, .gemini/skills/bio-microbiome-qiime2-workflow, .github/skills/bio-microbiome-qiime2-workflow and .opencode/skills/bio-microbiome-qiime2-workflow in your project.

What does Bio Microbiome Qiime2 Workflow need to run?

Going by SKILL.md and its folder, Bio Microbiome Qiime2 Workflow needs a shell for the scripts in its folder. Our summary lists: Python 3; A Bash shell.

Does Bio Microbiome Qiime2 Workflow access the network?

SKILL.md names 1 domain. In commands or code: data.qiime2.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Bio Microbiome Qiime2 Workflow safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Microbiome Qiime2 Workflow use?

No licence was found for Bio Microbiome Qiime2 Workflow or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Microbiome Qiime2 Workflow use?

About 1.6k tokens (SKILL.md is roughly 6.2k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Microbiome Qiime2 Workflow?

Skills that share tags, products or a category with Bio Microbiome Qiime2 Workflow: Qiime2 Amplicon (K-Dense-AI/scientific-agent-skills, 48k stars), Bio Microbiome Amplicon Processing (GPTomics/bioSkills, 1.2k stars), Bio Microbiome Qiime2 Workflow (GPTomics/bioSkills, 1.2k stars) and Waypoint Bio (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Microbiome Qiime2 Workflow?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.

Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.