pathogen-epi-genomics
Workflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill pathogen-epi-genomics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Pathogen Epidemiological Genomics ## Version Compatibility Reference examples assume recent stable releases of the preferred tools, especially `phylogenetics` and the other tools listed below. Before using code or command patterns, verify installed versions match the environment: - Python: `python -c "import <module>; print(<module>.__version__)"` - CLI: `<tool> --version` - If signatures differ, inspect the installed help or API and adapt the pattern instead of retrying unchanged. ## Overview Workflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis. ## When To Use This Skill - use when the task is pathogen surveillance, lineage assignment, or outbreak genomics - use when sample metadata include time, geography, or host context - use when genomic comparison must be linked to epidemiological interpretation ## Quick Route - If the input is raw or minimally processed data, start with validation and QC before any modeling. - If the input is already processed, skip directly to the first workflow step that matches the user goal. - If the user asks for a biological conclusion, always produce at least one QC or confid
- Version Compatibility
- Overview
- When To Use This Skill
- Quick Route
- Progressive Disclosure
- Default Rules
- Expected Inputs
- Expected Outputs
- Preferred Tools
- Starter Pattern
- Workflow
- 1. Standardize metadata
- 2. Generate comparable genomic summaries
- 3. Assign lineages or clusters
What does the pathogen-epi-genomics skill do?
Workflow for outbreak-style pathogen genomics, surveillance, lineage assignment, and transmission-oriented comparative analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill pathogen-epi-genomics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.