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Agent skill

Bio Epidemiological Genomics Pathogen Typing

by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA.

No licenceAuto-check passedResearch & Science

Install Bio Epidemiological Genomics Pathogen Typing

skills CLI
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-epidemiological-genomics-pathogen-typing -a claude-code

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

GitHub CLI
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-epidemiological-genomics-pathogen-typing --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-epidemiological-genomics-pathogen-typing .claude/skills/bio-epidemiological-genomics-pathogen-typing && 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-epidemiological-genomics-pathogen-typing
GitHub stars
3.1k
Used in
1 other repo
Token cost
~1.5k tokens
SKILL.md length
177 words
Files
3
Skills in repo
279
Repo updated
First seen
Licence
None found

At a glance

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA.

  • Identifying strain types
  • SKILL.md covers Version Compatibility, MLST with mlst Tool, Parse MLST Results and Core Genome MLST (cgMLST), plus 4 more sections
  • Runs Python scripts from its folder; calls pip and conda; reaches enterobase.warwick.ac.uk
  • Tracking outbreak clones

What it does

Bio Epidemiological Genomics Pathogen Typing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Use when identifying strain types, tracking outbreak clones, or characterizing bacterial isolates.

Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/mlst_typing.py` 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

  • Identifying strain types
  • Tracking outbreak clones
  • Characterizing bacterial isolates

Example prompts

  • “/bio-epidemiological-genomics-pathogen-typing”

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
    • conda

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • enterobase.warwick.ac.uk

    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 Epidemiological Genomics Pathogen Typing loads about 1.5k tokens when it runs. Until then it costs about 75 tokens; SKILL.md has 177 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~75
When it runs · the whole SKILL.md, loaded when a task matches
~1.5k

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 177 words (~1,532 tokens).

“Reference examples tested with: mlst 2.23+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, scipy 1.12+”

— opening of SKILL.md by FreedomIntelligence
name
bio-epidemiological-genomics-pathogen-typing
tool_type
cli
primary_tool
mlst

Read the full SKILL.md on GitHub

Files

SKILL.md and 2 other files in skills/bio-epidemiological-genomics-pathogen-typing of FreedomIntelligence/OpenClaw-Medical-Skills.

  • SKILL.md
  • examples/mlst_typing.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 9, 2026.

Compare with similar skills

Bio Epidemiological Genomics Pathogen Typing 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 Epidemiological Genomics Pathogen Typing compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Bio Epidemiological Genomics Pathogen Typing this skillFreedomIntelligence/OpenClaw-Medical-Skills3.1k1 repos~1.5kAutomated safety check: PassNone
Alphagenome Single Variant Analysisgoogle-deepmind/science-skills3.2k2 repos~3kAutomated safety check: NotesApache-2.0
13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills48k1 repos~3.2kAutomated safety check: PassMIT
Clinvar Databasegoogle-deepmind/science-skills3.2k2 repos~3.9kAutomated safety check: NotesApache-2.0
Metabolic Study Planneraiming-lab/AutoResearchClaw15k—~1.9kAutomated safety check: PassMIT
Dbsnp Databasegoogle-deepmind/science-skills3.2k2 repos~3.4kAutomated safety check: NotesApache-2.0

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Categories

Questions about Bio Epidemiological Genomics Pathogen Typing

What does Bio Epidemiological Genomics Pathogen Typing do?

Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA. Bio Epidemiological Genomics Pathogen Typing is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Perform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization using mlst and chewBBACA.

When should I use Bio Epidemiological Genomics Pathogen Typing?

Bio Epidemiological Genomics Pathogen Typing fits situations like: identifying strain types; tracking outbreak clones; characterizing bacterial isolates.

How do I install Bio Epidemiological Genomics Pathogen Typing in Claude Code?

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

How do I install Bio Epidemiological Genomics Pathogen Typing in Codex?

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

Can I use Bio Epidemiological Genomics Pathogen Typing 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-epidemiological-genomics-pathogen-typing -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-epidemiological-genomics-pathogen-typing, .gemini/skills/bio-epidemiological-genomics-pathogen-typing, .github/skills/bio-epidemiological-genomics-pathogen-typing and .opencode/skills/bio-epidemiological-genomics-pathogen-typing in your project.

What does Bio Epidemiological Genomics Pathogen Typing need to run?

Going by SKILL.md and its folder, Bio Epidemiological Genomics Pathogen Typing needs Python for the scripts in its folder and the command-line tools its instructions call (pip and conda). Our summary lists: Python 3.

Does Bio Epidemiological Genomics Pathogen Typing access the network?

SKILL.md names 1 domain. In commands or code: enterobase.warwick.ac.uk; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Bio Epidemiological Genomics Pathogen Typing 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 Epidemiological Genomics Pathogen Typing use?

No licence was found for Bio Epidemiological Genomics Pathogen Typing or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Bio Epidemiological Genomics Pathogen Typing use?

About 1.5k tokens (SKILL.md is roughly 6.1k 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 Epidemiological Genomics Pathogen Typing?

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

Who maintains Bio Epidemiological Genomics Pathogen Typing?

FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 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.