Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Agent skill
Fastq Analysis Pipeline
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and…
Install Fastq Analysis Pipeline
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill fastq-analysis-pipeline -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills fastq-analysis-pipeline --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/fastq-analysis .claude/skills/fastq-analysis-pipeline && 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 "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .claude/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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/fastq-analysisType 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 fastq-analysis-pipeline -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills fastq-analysis-pipeline --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/fastq-analysis .agents/skills/fastq-analysis-pipeline && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .agents/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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 fastq-analysis-pipeline -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills fastq-analysis-pipeline --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/fastq-analysis .cursor/skills/fastq-analysis-pipeline && 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 "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .cursor/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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/fastq-analysis--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 fastq-analysis-pipeline -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills fastq-analysis-pipeline --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/fastq-analysis .gemini/skills/fastq-analysis-pipeline && 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 "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .gemini/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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 fastq-analysis-pipelineInstalls 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 fastq-analysis-pipeline -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/fastq-analysis .github/skills/fastq-analysis-pipeline && 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 "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .github/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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 fastq-analysis-pipeline -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 fastq-analysis-pipeline --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/fastq-analysis .opencode/skills/fastq-analysis-pipeline && 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 "fastq-analysis-pipeline" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/fastq-analysis into .opencode/skills/fastq-analysis-pipeline/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "fastq-analysis-pipeline", 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
fastq-analysis-pipeline- GitHub stars
- 3.1k
- Used in
- 2 other repos
- Token cost
- ~2k tokens
- SKILL.md length
- 560 words
- Files
- 2
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and…
- Works in 10 steps: Environment setup → SRA data download (ov.alignment.prefetch… → FASTQ quality control (ov.alignment.fastp) → …
- Tasks that involve Bioinformatics
- SKILL.md covers Overview, Instructions, Critical API Reference and Examples, plus 1 more section
- Calls pip
What it does
Fastq Analysis Pipeline is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `reference.md`).
It sits in Research & Science, covering Bioinformatics. It works with Python. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/fastq-analysis-pipeline”
Requirements
- Python 3
Workflow steps
10 steps, taken from the first numbered list in SKILL.md.
- Environment setup
- SRA data download (ov.alignment.prefetch + ov.alignment.fqdump)
- FASTQ quality control (ov.alignment.fastp)
- STAR alignment (ov.alignment.STAR)
- Gene quantification (ov.alignment.featureCount)
- Single-cell path (ov.alignment.ref + ov.alignment.count)
- Wiring fastp output into STAR input
- Wiring STAR output into featureCount input
- Skipping completed steps
- Troubleshooting
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
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
Fastq Analysis Pipeline loads about 2k tokens when it runs. Until then it costs about 61 tokens; SKILL.md has 560 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 560 words (~2,000 tokens).
“OmicVerse provides a complete FASTQ-to-count-matrix pipeline via the ov.alignment module. This skill covers:”
- name
- fastq-analysis-pipeline
- title
- FASTQ analysis and RNA-seq alignment with omicverse
Files
SKILL.md and 1 other file in skills/fastq-analysis of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- reference.md
Open the folder on GitHubat commit b1f9b6e
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 9, 2026.
Compare with similar skills
Fastq Analysis Pipeline 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 |
|---|---|---|---|---|---|---|
| Fastq Analysis Pipeline this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 2 repos | ~2k | Automated safety check: Pass | None | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Singlecell Qcxuzhougeng/wisp-science | 1k | — | ~1.6k | Automated safety check: Pass | AGPL-3.0 | |
| Trackplotygidtu/trackplot | 109 | — | ~1.9k | Automated safety check: Pass | BSD-3-Clause | |
| UniProt Database Accessdavila7/claude-code-templates | 32k | 14 repos | ~1.7k | Automated safety check: Pass | MIT |
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Singlecell Qc
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A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.
Trackplot
ygidtu/trackplot
Generate sashimi-style genome visualization plots (coverage, line, heatmap, IGV read-by-read, HiC, circRNA, motif) from BAM/bigWig/depth/HiC inputs.
UniProt Database Access
davila7/claude-code-templates
Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.
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End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
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Related
Works with
Categories
Questions about Fastq Analysis Pipeline
What does Fastq Analysis Pipeline do?
Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and…. Fastq Analysis Pipeline is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Guide through omicverse's alignment module for SRA downloading, FASTQ quality control, STAR alignment, gene quantification, and single-cell kallisto/bustools pipelines covering both bulk and single-cell RNA-seq workflows.
When should I use Fastq Analysis Pipeline?
Fastq Analysis Pipeline fits situations like: tasks that involve Bioinformatics.
How do I install Fastq Analysis Pipeline in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill fastq-analysis-pipeline -a claude-code`. Or copy the skill folder (skills/fastq-analysis in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/fastq-analysis-pipeline in your project. Claude Code loads it when a task matches its description.
How do I install Fastq Analysis Pipeline in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill fastq-analysis-pipeline -a codex`. Or copy the skill folder (skills/fastq-analysis in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/fastq-analysis-pipeline in your project. Codex loads it when a task matches its description.
Can I use Fastq Analysis Pipeline 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 fastq-analysis-pipeline -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/fastq-analysis-pipeline, .gemini/skills/fastq-analysis-pipeline, .github/skills/fastq-analysis-pipeline and .opencode/skills/fastq-analysis-pipeline in your project.
What does Fastq Analysis Pipeline need to run?
Going by SKILL.md and its folder, Fastq Analysis Pipeline needs the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Fastq Analysis Pipeline 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 Fastq Analysis Pipeline 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 Fastq Analysis Pipeline use?
No licence was found for Fastq Analysis Pipeline or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Fastq Analysis Pipeline use?
About 2k tokens (SKILL.md is roughly 8k 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 Fastq Analysis Pipeline?
Skills that share tags, products or a category with Fastq Analysis Pipeline: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Singlecell Qc (xuzhougeng/wisp-science, 1k stars) and Trackplot (ygidtu/trackplot, 109 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Fastq Analysis Pipeline?
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.