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pathogen-epi-genomics

Automate pathogen genomics surveillance, lineage assignment, and comparative outbreak analysis.

25|5|Updated Mar 22, 2026
Search Tags:#genomics#epidemiology#lineage#phylogenetics#surveillance#outbreak#pathogen
One-click install
npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill pathogen-epi-genomics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pathogen-epi-genomics
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/metagenomics-and-microbiome/pathogen-epi-genomics
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill pathogen-epi-genomics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

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.

Frequently Asked Questions about pathogen-epi-genomics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate pathogen genomics surveillance for outbreak investigations?▼

Pathogen genomics surveillance is automated by standardizing collection metadata, generating comparable genomic summaries, and assigning lineages to produce transmission-oriented outbreak tables and figures using Python-based tooling.

What is lineage assignment and how does it work with pathogen genomes?▼

Lineage assignment for pathogen genomes works by generating comparable variant or consensus summaries from raw reads and assigning them to distinct lineages to inform transmission networks during outbreaks.

Do I need collection metadata to run outbreak genomics comparative analysis?▼

Yes, collection metadata is required to run outbreak genomics comparative analysis, as the workflow standardizes time, location, and sample identifiers to integrate epidemiological context with pathogen genomes.

Can I use this workflow for pathogen surveillance across different locations and time periods?▼

Yes, you can use this workflow for pathogen surveillance across different locations and time periods, as it standardizes collection metadata and integrates epidemiological context to compare samples across time and location.

What outputs does the pathogen epidemiology genomics workflow generate?▼

The pathogen epidemiology genomics workflow generates surveillance-ready tables and figures that combine lineage assignments, comparable genomic summaries, and standardized epidemiological metadata for outbreak analysis.

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