Convert
remotion-dev/remotion
Start the local @remotion/convert app and open it in the Codex browser.
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller.
No licenceAuto-check passed
Install Bio Basecalling
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-basecalling --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-basecalling .claude/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .claude/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecallingType 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-basecalling -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-basecalling --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-basecalling .agents/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .agents/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecalling -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-basecalling --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-basecalling .cursor/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .cursor/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecalling--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-basecalling -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-basecalling --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-basecalling .gemini/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .gemini/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecallingInstalls 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-basecalling -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-basecalling .github/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .github/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecalling -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-basecalling --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-basecalling .opencode/skills/bio-basecalling && 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-basecalling" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling into .opencode/skills/bio-basecalling/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-basecalling", 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-basecalling- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2k tokens
- SKILL.md length
- 384 words
- Files
- 4
- Skills in repo
- 173
- Repo updated
- First seen
- Licence
- None found
At a glance
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller.
- Processing raw Nanopore data before alignment
- SKILL.md covers Version Compatibility, Dorado (Recommended), Guppy (Deprecated - Legacy Only) and POD5 File Handling
- Runs Shell scripts from its folder
What it does
Bio Basecalling is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.
Its SKILL.md is about 2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files (for example `examples/basecall_pipeline.sh`, `examples/dorado_basecall.sh` and `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Processing raw Nanopore data before alignment
Example prompts
- “/bio-basecalling”
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 Basecalling loads about 2k tokens when it runs. Until then it costs about 78 tokens; SKILL.md has 384 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 384 words (~2,039 tokens).
“Reference examples tested with: samtools 1.19+”
- name
- bio-basecalling
- tool_type
- cli
- primary_tool
- dorado
Files
SKILL.md and 3 other files in skills/bio-basecalling of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/basecall_pipeline.sh
- examples/dorado_basecall.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 Basecalling 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 Basecalling this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2k | Automated safety check: Pass | None | |
| Convertremotion-dev/remotion | 62k | — | ~247 | Automated safety check: Pass | Custom licence | |
| Bio Long Read Sequencing BasecallingGPTomics/bioSkills | 1.2k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Trader Signalruvnet/ruflo | 74k | — | ~605 | Automated safety check: Notes | MIT | |
| Waypoint BioK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~4.2k | Automated safety check: Pass | MIT | |
| Agent Signal Pipelinelobehub/lobehub | 83k | — | ~1.7k | Automated safety check: Pass | Custom licence |
Similar skills
- Official
Bio Long Read Sequencing Basecalling
GPTomics/bioSkills
Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accuracy tier (fast/hac/sup), requesting modified bases (5mCG5hmCG, 6mA, m6A) at…
Trader Signal
ruvnet/ruflo
Generate trading signals using npx neural-trader anomaly detection engine with Z-score scoring and neural prediction
Waypoint Bio
K-Dense-AI/scientific-agent-skills
Supports work with Outpost Bio's open microbiome foundation models - the Waypoint checkpoints (Waypoint-6m, Waypoint-45m, Waypoint-170m), the Atlas pretraining corpus, the Compass eight-task…
Agent Signal Pipeline
lobehub/lobehub
Guides building event-driven background work for LobeHub agents, with sources, signals, actions, policies, workflow handoff and deduplication.
- Official
Signal Write
github/awesome-copilot
Emit structured agent signals — hands-up, blocked, done, checkpoint, partnership.
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Questions about Bio Basecalling
What does Bio Basecalling do?
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Bio Basecalling is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller.
When should I use Bio Basecalling?
Bio Basecalling fits situations like: processing raw Nanopore data before alignment.
How do I install Bio Basecalling in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -a claude-code`. Or copy the skill folder (skills/bio-basecalling in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-basecalling in your project. Claude Code loads it when a task matches its description.
How do I install Bio Basecalling in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -a codex`. Or copy the skill folder (skills/bio-basecalling in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-basecalling in your project. Codex loads it when a task matches its description.
Can I use Bio Basecalling 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-basecalling -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-basecalling, .gemini/skills/bio-basecalling, .github/skills/bio-basecalling and .opencode/skills/bio-basecalling in your project.
What does Bio Basecalling need to run?
Going by SKILL.md and its folder, Bio Basecalling needs a shell for the scripts in its folder. Our summary lists: A Bash shell.
Does Bio Basecalling 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 Basecalling 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 Basecalling use?
No licence was found for Bio Basecalling or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Basecalling use?
About 2k tokens (SKILL.md is roughly 8.2k 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 Basecalling?
Skills that share tags, products or a category with Bio Basecalling: Convert (remotion-dev/remotion, 62k stars), Bio Long Read Sequencing Basecalling (GPTomics/bioSkills, 1.2k stars), Trader Signal (ruvnet/ruflo, 74k stars) and Waypoint Bio (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Basecalling?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 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.