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Agent skill

Bio Methylation Bismark Alignment

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2.

No licenceAuto-check passedResearch & Science

Install Bio Methylation Bismark Alignment

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-methylation-bismark-alignment -a claude-code

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

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-methylation-bismark-alignment --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-methylation-bismark-alignment .claude/skills/bio-methylation-bismark-alignment && 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-methylation-bismark-alignment
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.4k tokens
SKILL.md length
224 words
Files
3
Skills in repo
170
Repo updated
First seen
Licence
None found

At a glance

Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2.

  • Other bisulfite-converted sequencing reads to a reference genome
  • SKILL.md covers Version Compatibility, Prepare Genome Index, Basic Single-End Alignment and Paired-End Alignment, plus 14 more sections
  • Runs Shell scripts from its folder
  • Tasks that involve Bioinformatics

What it does

Bio Methylation Bismark Alignment is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.

Its SKILL.md is about 1.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/bismark_basic.sh` and `usage-guide.md`).

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

When your agent uses it

  • Other bisulfite-converted sequencing reads to a reference genome
  • Tasks that involve Bioinformatics

Example prompts

  • “/bio-methylation-bismark-alignment”

Requirements

  • 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

    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 Methylation Bismark Alignment loads about 1.4k tokens when it runs. Until then it costs about 71 tokens; SKILL.md has 224 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~71
When it runs · the whole SKILL.md, loaded when a task matches
~1.4k

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 224 words (~1,373 tokens).

“Reference examples tested with: Bowtie2 2.5.3+, HISAT2 2.2.1+, Trim Galore 0.6.10+, samtools 1.19+”

— opening of SKILL.md by FreedomIntelligence
name
bio-methylation-bismark-alignment
tool_type
cli
primary_tool
bismark

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-methylation-bismark-alignment of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/bismark_basic.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 Methylation Bismark Alignment 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 Methylation Bismark Alignment compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Methylation Bismark Alignment this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.4kAutomated safety check: PassNone
Dbsnp Databasegoogle-deepmind/science-skills3.2k3 repos~3.4kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
MFA Pipeline Orchestratoraiming-lab/AutoResearchClaw15k—~923Automated safety check: PassMIT

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Categories

Questions about Bio Methylation Bismark Alignment

What does Bio Methylation Bismark Alignment do?

Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Bio Methylation Bismark Alignment is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2.

When should I use Bio Methylation Bismark Alignment?

Bio Methylation Bismark Alignment fits situations like: other bisulfite-converted sequencing reads to a reference genome; tasks that involve Bioinformatics.

How do I install Bio Methylation Bismark Alignment in Claude Code?

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

How do I install Bio Methylation Bismark Alignment in Codex?

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

Can I use Bio Methylation Bismark Alignment 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-methylation-bismark-alignment -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-methylation-bismark-alignment, .gemini/skills/bio-methylation-bismark-alignment, .github/skills/bio-methylation-bismark-alignment and .opencode/skills/bio-methylation-bismark-alignment in your project.

What does Bio Methylation Bismark Alignment need to run?

Going by SKILL.md and its folder, Bio Methylation Bismark Alignment needs a shell for the scripts in its folder. Our summary lists: A Bash shell.

Does Bio Methylation Bismark Alignment 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 Methylation Bismark Alignment 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 Methylation Bismark Alignment use?

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

How many tokens does Bio Methylation Bismark Alignment use?

About 1.4k tokens (SKILL.md is roughly 5.5k 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 Methylation Bismark Alignment?

Skills that share tags, products or a category with Bio Methylation Bismark Alignment: Dbsnp Database (google-deepmind/science-skills, 3.2k stars), Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Methylation Bismark Alignment?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,052 GitHub stars. The repository holds 170 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.