GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Agent skill
Bio Cfdna Preprocessing
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio.
Install Bio Cfdna Preprocessing
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-cfdna-preprocessing --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-cfdna-preprocessing .claude/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .claude/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessingType 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-cfdna-preprocessing -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-cfdna-preprocessing --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-cfdna-preprocessing .agents/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .agents/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessing -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-cfdna-preprocessing --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-cfdna-preprocessing .cursor/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .cursor/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessing--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-cfdna-preprocessing -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-cfdna-preprocessing --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-cfdna-preprocessing .gemini/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .gemini/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessingInstalls 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-cfdna-preprocessing -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-cfdna-preprocessing .github/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .github/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessing -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-cfdna-preprocessing --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-cfdna-preprocessing .opencode/skills/bio-cfdna-preprocessing && 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-cfdna-preprocessing" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-cfdna-preprocessing into .opencode/skills/bio-cfdna-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-cfdna-preprocessing", 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-cfdna-preprocessing- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~1.6k tokens
- SKILL.md length
- 250 words
- Files
- 3
- Skills in repo
- 170
- Repo updated
- First seen
- Licence
- None found
At a glance
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio.
- Processing plasma cfDNA sequencing data before downstream analysis
- SKILL.md covers Version Compatibility, Pre-Analytical Considerations, UMI-Aware Pipeline with fgbio and Python Implementation, plus 3 more sections
- Runs Python scripts from its folder; calls pip
What it does
Bio Cfdna Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
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/preprocess_cfdna.py` and `usage-guide.md`).
It sits in Research & Science. It works with Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Processing plasma cfDNA sequencing data before downstream analysis
Example prompts
- “Use the bio-cfdna-preprocessing skill to preprocess cell-free DNA sequencing data including adapter trimming, alignment optimized for short…”
- “/bio-cfdna-preprocessing”
Requirements
- Python 3
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 (Python), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use 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 Cfdna Preprocessing loads about 1.6k tokens when it runs. Until then it costs about 83 tokens; SKILL.md has 250 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 250 words (~1,604 tokens).
“Reference examples tested with: BWA 0.7.17+, fgbio 2.1+, matplotlib 3.8+, numpy 1.26+, pysam 0.22+, samtools 1.19+”
- name
- bio-cfdna-preprocessing
- tool_type
- python
- primary_tool
- fgbio
Files
SKILL.md and 2 other files in skills/bio-cfdna-preprocessing of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/preprocess_cfdna.py
- 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 Cfdna Preprocessing 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 Cfdna Preprocessing this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.6k | Automated safety check: Pass | None | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Last30daysmvanhorn/last30days-skill | 64k | — | ~7.8k | Automated safety check: Notes | MIT | |
| NetworkxzLanqing/codex-claude-academic-skills | 4.6k | 16 repos | ~3.2k | Automated safety check: Pass | BSD-3-Clause | |
| Nature-Style Scientific FiguresYuan1z0825/nature-skills | 46k | — | ~2.9k | Automated safety check: Pass | Apache-2.0 | |
| Citation ManagementK-Dense-AI/claude-scientific-writer | 2.4k | 3 repos | ~3.9k | Automated safety check: Notes | MIT |
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Related
Works with
Categories
Questions about Bio Cfdna Preprocessing
What does Bio Cfdna Preprocessing do?
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Bio Cfdna Preprocessing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio.
When should I use Bio Cfdna Preprocessing?
Bio Cfdna Preprocessing fits situations like: processing plasma cfDNA sequencing data before downstream analysis.
How do I install Bio Cfdna Preprocessing in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -a claude-code`. Or copy the skill folder (skills/bio-cfdna-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-cfdna-preprocessing in your project. Claude Code loads it when a task matches its description.
How do I install Bio Cfdna Preprocessing in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-cfdna-preprocessing -a codex`. Or copy the skill folder (skills/bio-cfdna-preprocessing in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-cfdna-preprocessing in your project. Codex loads it when a task matches its description.
Can I use Bio Cfdna Preprocessing 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-cfdna-preprocessing -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-cfdna-preprocessing, .gemini/skills/bio-cfdna-preprocessing, .github/skills/bio-cfdna-preprocessing and .opencode/skills/bio-cfdna-preprocessing in your project.
What does Bio Cfdna Preprocessing need to run?
Going by SKILL.md and its folder, Bio Cfdna Preprocessing needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Cfdna Preprocessing access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Cfdna Preprocessing 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 Cfdna Preprocessing use?
No licence was found for Bio Cfdna Preprocessing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Cfdna Preprocessing use?
About 1.6k tokens (SKILL.md is roughly 6.4k 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 Cfdna Preprocessing?
Skills that share tags, products or a category with Bio Cfdna Preprocessing: GitHub Deep Research (bytedance/deer-flow, 83k stars), Last30days (mvanhorn/last30days-skill, 64k stars), Networkx (zLanqing/codex-claude-academic-skills, 4.6k stars) and Nature-Style Scientific Figures (Yuan1z0825/nature-skills, 46k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Cfdna Preprocessing?
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.