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Agent skill

Bio Long Read Sequencing Clair3 Variants

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels.

No licenceAuto-check passedResearch & Science

Install Bio Long Read Sequencing Clair3 Variants

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-long-read-sequencing-clair3-variants -a claude-code

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

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-long-read-sequencing-clair3-variants --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-long-read-sequencing-clair3-variants .claude/skills/bio-long-read-sequencing-clair3-variants && 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-long-read-sequencing-clair3-variants
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.8k tokens
SKILL.md length
293 words
Files
3
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels.

  • Calling germline variants from ONT
  • SKILL.md covers Version Compatibility, Basic Usage, Platform-Specific Models and Key Parameters, plus 9 more sections
  • Runs Shell scripts from its folder; calls docker and pip
  • PacBio alignments

What it does

Bio Long Read Sequencing Clair3 Variants is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications.

Its SKILL.md is about 1.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/clair3_workflow.sh` and `usage-guide.md`).

It sits in Research & Science, covering Bioinformatics and Deep learning. It works with Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.

When your agent uses it

  • Calling germline variants from ONT
  • PacBio alignments
  • Particularly when high accuracy is needed for clinical
  • Research applications

Example prompts

  • “/bio-long-read-sequencing-clair3-variants”

Requirements

  • Python 3
  • A Bash shell
  • Docker

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.

    Shell commands in SKILL.md call:

    • docker
    • pip

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

  • Network

    No URLs in SKILL.md. Its commands use docker and pip, which can reach the network depending on how they are called.

    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 Long Read Sequencing Clair3 Variants loads about 1.8k tokens when it runs. Until then it costs about 70 tokens; SKILL.md has 293 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~70
When it runs · the whole SKILL.md, loaded when a task matches
~1.8k

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 293 words (~1,847 tokens).

“Reference examples tested with: DeepVariant 1.6+, Entrez Direct 21.0+, bcftools 1.19+, minimap2 2.26+”

— opening of SKILL.md by FreedomIntelligence
name
bio-long-read-sequencing-clair3-variants
tool_type
cli
primary_tool
Clair3

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-long-read-sequencing-clair3-variants of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/clair3_workflow.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 9, 2026.

Compare with similar skills

Bio Long Read Sequencing Clair3 Variants 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 Long Read Sequencing Clair3 Variants compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
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Alphagenome Predictionsgenomicsxai/alphagenome-pytorch162—~868Automated safety check: PassApache-2.0
Bio Atac Seq Deep Learning AtacGPTomics/bioSkills1.2k2 repos~5kAutomated safety check: PassMIT
Bio Clip Seq Clip Deep LearningGPTomics/bioSkills1.2k2 repos~4.7kAutomated safety check: PassMIT
Bio Chipseq Chip Deep LearningGPTomics/bioSkills1.2k2 repos~3.8kAutomated safety check: PassMIT

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Works with

Categories

Questions about Bio Long Read Sequencing Clair3 Variants

What does Bio Long Read Sequencing Clair3 Variants do?

Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Bio Long Read Sequencing Clair3 Variants is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels.

When should I use Bio Long Read Sequencing Clair3 Variants?

Bio Long Read Sequencing Clair3 Variants fits situations like: calling germline variants from ONT; pacBio alignments; particularly when high accuracy is needed for clinical; research applications.

How do I install Bio Long Read Sequencing Clair3 Variants in Claude Code?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-long-read-sequencing-clair3-variants -a claude-code`. Or copy the skill folder (skills/bio-long-read-sequencing-clair3-variants in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-long-read-sequencing-clair3-variants in your project. Claude Code loads it when a task matches its description.

How do I install Bio Long Read Sequencing Clair3 Variants in Codex?

Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-long-read-sequencing-clair3-variants -a codex`. Or copy the skill folder (skills/bio-long-read-sequencing-clair3-variants in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-long-read-sequencing-clair3-variants in your project. Codex loads it when a task matches its description.

Can I use Bio Long Read Sequencing Clair3 Variants 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-long-read-sequencing-clair3-variants -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-long-read-sequencing-clair3-variants, .gemini/skills/bio-long-read-sequencing-clair3-variants, .github/skills/bio-long-read-sequencing-clair3-variants and .opencode/skills/bio-long-read-sequencing-clair3-variants in your project.

What does Bio Long Read Sequencing Clair3 Variants need to run?

Going by SKILL.md and its folder, Bio Long Read Sequencing Clair3 Variants needs a shell for the scripts in its folder and the command-line tools its instructions call (docker and pip). Our summary lists: Python 3; A Bash shell; Docker.

Does Bio Long Read Sequencing Clair3 Variants access the network?

SKILL.md contains no URLs. Its commands use docker and pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.

Is Bio Long Read Sequencing Clair3 Variants 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 Long Read Sequencing Clair3 Variants use?

No licence was found for Bio Long Read Sequencing Clair3 Variants or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Long Read Sequencing Clair3 Variants use?

About 1.8k tokens (SKILL.md is roughly 7.4k 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 Long Read Sequencing Clair3 Variants?

Skills that share tags, products or a category with Bio Long Read Sequencing Clair3 Variants: Pixi Environment Builder (xuzhougeng/wisp-science, 1k stars), Alphagenome Predictions (genomicsxai/alphagenome-pytorch, 162 stars), Bio Atac Seq Deep Learning Atac (GPTomics/bioSkills, 1.2k stars) and Bio Clip Seq Clip Deep Learning (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 Long Read Sequencing Clair3 Variants?

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.