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