Polish assemblies and call variants from Oxford Nanopore data using medaka.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-longread-medaka --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-longread-medaka .claude/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .claude/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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-longread-medakaType 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-longread-medaka -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-longread-medaka --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-longread-medaka .agents/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .agents/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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-longread-medaka -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-longread-medaka --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-longread-medaka .cursor/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .cursor/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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-longread-medaka--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-longread-medaka -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-longread-medaka --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-longread-medaka .gemini/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .gemini/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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-longread-medakaInstalls 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-longread-medaka -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-longread-medaka .github/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .github/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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-longread-medaka -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-longread-medaka --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-longread-medaka .opencode/skills/bio-longread-medaka && 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-longread-medaka" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka into .opencode/skills/bio-longread-medaka/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-longread-medaka", 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.
bio-longread-medakaPolish assemblies and call variants from Oxford Nanopore data using medaka.
Bio Longread Medaka is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.
Its SKILL.md is about 1.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/medaka_polish.sh`, `examples/medaka_variant.sh` and `usage-guide.md`).
It sits in AI & LLM Engineering, covering Deep learning and Bioinformatics. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.
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.
Ships script files (Shell), which the agent can run.
From the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
github.comFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Bio Longread Medaka loads about 1.3k tokens when it runs. Until then it costs about 66 tokens; SKILL.md has 273 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.
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.
Without a licence we can't republish the file, so here is its outline and opening line. It has 273 words (~1,267 tokens).
“Reference examples tested with: bcftools 1.19+, minimap2 2.26+, samtools 1.19+”
SKILL.md and 3 other files in skills/bio-longread-medaka of FreedomIntelligence/OpenClaw-Medical-Skills.
Open the folder on GitHubat commit b1f9b6e
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.
Bio Longread Medaka 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 Longread Medaka this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~1.3k | Automated safety check: Pass | None | |
| Alphagenome Predictionsgenomicsxai/alphagenome-pytorch | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 | |
| Bio Atac Seq Deep Learning AtacGPTomics/bioSkills | 1.2k | 2 repos | ~5k | Automated safety check: Pass | MIT | |
| Bio Clip Seq Clip Deep LearningGPTomics/bioSkills | 1.2k | 2 repos | ~4.7k | Automated safety check: Pass | MIT | |
| Bio Chipseq Chip Deep LearningGPTomics/bioSkills | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT | |
| tangermeme Genomic Model Analysisjmschrei/tangermeme | 316 | — | ~1.6k | Automated safety check: Pass | MIT |
genomicsxai/alphagenome-pytorch
Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant…
GPTomics/bioSkills
Sequence-based deep learning for ATAC-seq using chromBPNet, BPNet, scBasset, or Enformer.
GPTomics/bioSkills
Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect…
GPTomics/bioSkills
Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data.
jmschrei/tangermeme
Routes agents to the right tangermeme reference for analyzing trained genomic deep learning models, from attributions and motif experiments to variant effects and design.
genomicsxai/alphagenome-pytorch
Fine-tune or transfer-learn AlphaGenome-PyTorch on custom genomic data — pick a mode (linear probe, LoRA, Locon, full), train on BigWig tracks with agt finetune, use adapters, delta checkpoints…
FreedomIntelligence/OpenClaw-Medical-Skills
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
FreedomIntelligence/OpenClaw-Medical-Skills
Select and apply numerical differentiation schemes for PDE/ODE discretization.
FreedomIntelligence/OpenClaw-Medical-Skills
FHIR API development guide for building healthcare endpoints.
FreedomIntelligence/OpenClaw-Medical-Skills
Select and configure linear solvers for systems Ax=b in dense and sparse problems.
FreedomIntelligence/OpenClaw-Medical-Skills
Query 14+ biomedical databases for drug repurposing, target discovery, clinical trials, and literature research.
FreedomIntelligence/OpenClaw-Medical-Skills
Plan and evaluate mesh generation for numerical simulations.
Categories
Polish assemblies and call variants from Oxford Nanopore data using medaka. Bio Longread Medaka is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Polish assemblies and call variants from Oxford Nanopore data using medaka.
Bio Longread Medaka fits situations like: improving ONT-only assemblies; calling variants from Nanopore data without short-read polishing.
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka -a claude-code`. Or copy the skill folder (skills/bio-longread-medaka in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-longread-medaka in your project. Claude Code loads it when a task matches its description.
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka -a codex`. Or copy the skill folder (skills/bio-longread-medaka in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-longread-medaka in your project. Codex loads it when a task matches its description.
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-longread-medaka -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-longread-medaka, .gemini/skills/bio-longread-medaka, .github/skills/bio-longread-medaka and .opencode/skills/bio-longread-medaka in your project.
Going by SKILL.md and its folder, Bio Longread Medaka needs a shell for the scripts in its folder. Our summary lists: A Bash shell.
SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.
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.
No licence was found for Bio Longread Medaka or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
About 1.3k tokens (SKILL.md is roughly 5.1k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Bio Longread Medaka: Alphagenome Predictions (genomicsxai/alphagenome-pytorch, 162 stars), Bio Atac Seq Deep Learning Atac (GPTomics/bioSkills, 1.2k stars), Bio Clip Seq Clip Deep Learning (GPTomics/bioSkills, 1.2k stars) and Bio Chipseq Chip 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.
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.
