Bio Microbiome Amplicon Processing
GPTomics/bioSkills
Infers exact amplicon sequence variants (ASVs) from demultiplexed 16S rRNA or ITS amplicon FASTQ with DADA2 - removing primers with cutadapt (--discard-untrimmed), learning a per-run error model…
Agent skill
Bio Microbiome Amplicon Processing
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2.
No licenceAuto-check passed
Install Bio Microbiome Amplicon Processing
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processing --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ 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-amplicon-processing .claude/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.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/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .claude/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processingType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processing --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-microbiome-amplicon-processing .agents/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .agents/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processing --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-microbiome-amplicon-processing .cursor/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .cursor/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-microbiome-amplicon-processing--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processing --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-microbiome-amplicon-processing .gemini/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .gemini/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processingInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-microbiome-amplicon-processing .github/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .github/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-microbiome-amplicon-processing --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-microbiome-amplicon-processing .opencode/skills/bio-microbiome-amplicon-processing && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-microbiome-amplicon-processing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-microbiome-amplicon-processing into .opencode/skills/bio-microbiome-amplicon-processing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-microbiome-amplicon-processing", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bio-microbiome-amplicon-processing- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.1k tokens
- SKILL.md length
- 167 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2.
- Processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis
- SKILL.md covers Version Compatibility, Complete DADA2 Workflow, Quality Filtering and Trimming and Error Rate Learning, plus 7 more sections
- Runs R scripts from its folder
What it does
Bio Microbiome Amplicon Processing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering, error learning, denoising, and chimera removal. Use when processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis
Example prompts
- “/bio-microbiome-amplicon-processing”
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 (R), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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 Amplicon Processing loads about 1.1k tokens when it runs. Until then it costs about 77 tokens; SKILL.md has 167 words of instructions outside code blocks.
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 167 words (~1,093 tokens).
“Reference examples tested with: DADA2 1.30+, cutadapt 4.4+”
- name
- bio-microbiome-amplicon-processing
- tool_type
- r
- primary_tool
- dada2
Files
SKILL.md and 2 other files in skills/bio-microbiome-amplicon-processing of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/dada2_workflow.R
- 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 9, 2026.
Compare with similar skills
Bio Microbiome Amplicon Processing 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Microbiome Amplicon Processing this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.1k | Automated safety check: Pass | None | |
| Bio Microbiome Amplicon ProcessingGPTomics/bioSkills | 1.2k | 1 repos | ~5.7k | Automated safety check: Pass | MIT | |
| Bio Long Read Sequencing Structural VariantsGPTomics/bioSkills | 1.2k | 1 repos | ~3.4k | Automated safety check: Pass | MIT | |
| Bio Long Read Sequencing Clair3 VariantsGPTomics/bioSkills | 1.2k | 1 repos | ~2.9k | Automated safety check: Pass | MIT | |
| Bio Variant Calling Structural Variant CallingGPTomics/bioSkills | 1.2k | 1 repos | ~7.2k | Automated safety check: Pass | MIT | |
| Bio Consensus SequencesGPTomics/bioSkills | 1.2k | 1 repos | ~4k | Automated safety check: Pass | MIT |
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Call structural variants (=50 bp deletions, insertions, inversions, duplications, translocations) from short- or long-read data by reconstructing four orthogonal signals (discordant pairs, split…
Bio Consensus Sequences
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Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar.
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Questions about Bio Microbiome Amplicon Processing
What does Bio Microbiome Amplicon Processing do?
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Bio Microbiome Amplicon Processing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2.
When should I use Bio Microbiome Amplicon Processing?
Bio Microbiome Amplicon Processing fits situations like: processing demultiplexed amplicon FASTQ files to generate an ASV table for downstream analysis.
How do I install Bio Microbiome Amplicon Processing in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a claude-code`. Or copy the skill folder (skills/bio-microbiome-amplicon-processing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-microbiome-amplicon-processing in your project. Claude Code loads it when a task matches its description.
How do I install Bio Microbiome Amplicon Processing in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-microbiome-amplicon-processing -a codex`. Or copy the skill folder (skills/bio-microbiome-amplicon-processing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-microbiome-amplicon-processing in your project. Codex loads it when a task matches its description.
Can I use Bio Microbiome Amplicon Processing 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-amplicon-processing -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-amplicon-processing, .gemini/skills/bio-microbiome-amplicon-processing, .github/skills/bio-microbiome-amplicon-processing and .opencode/skills/bio-microbiome-amplicon-processing in your project.
What does Bio Microbiome Amplicon Processing need to run?
Going by SKILL.md and its folder, Bio Microbiome Amplicon Processing needs R for the scripts in its folder.
Does Bio Microbiome Amplicon Processing access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Bio Microbiome Amplicon Processing 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 Amplicon Processing use?
No licence was found for Bio Microbiome Amplicon Processing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Microbiome Amplicon Processing use?
About 1.1k tokens (SKILL.md is roughly 4.4k 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 Amplicon Processing?
Skills that share tags, products or a category with Bio Microbiome Amplicon Processing: Bio Microbiome Amplicon Processing (GPTomics/bioSkills, 1.2k stars), Bio Long Read Sequencing Structural Variants (GPTomics/bioSkills, 1.2k stars), Bio Long Read Sequencing Clair3 Variants (GPTomics/bioSkills, 1.2k stars) and Bio Variant Calling Structural Variant Calling (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Microbiome Amplicon Processing?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 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.