pathogen-epi-genomics
CommunityOutbreak genomics and surveillance workflow
Authorzongtingwei
Version1.0.0
Installs0
System Documentation
What problem does it solve?
Workflow automates outbreak-style pathogen genomics analysis, enabling rapid surveillance, lineage assignment, and transmission-oriented comparison across samples.
Core Features & Use Cases
- Standardized metadata workflows: ensures time, location, and sample identifiers are consistent for downstream analysis.
- Genomic summaries & lineage calling: produces comparable variant or consensus summaries and assigns lineages.
- Use Case: Apply to outbreak investigations where genomes and related metadata inform transmission networks.
Quick Start
Run a baseline outbreak-genomics workflow on your pathogen dataset to obtain lineage calls and outbreak summaries.
Dependency Matrix
Required Modules
None requiredComponents
references
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: pathogen-epi-genomics Download link: https://github.com/zongtingwei/Bioclaw_Skills_Hub/archive/main.zip#pathogen-epi-genomics Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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