kibet-gilbert/rvfv-ngs-surveillance
Domain:
healthcareRecord type:
project
Creator:
Kib
Host:
Training tutorials and materials for NGS data analysis
# NGS-Based Pathogen Surveillance: RVFV as a Case Study
**A comprehensive lecture series and practical guide to genomic epidemiology for emerging infectious diseases**
---
## 📖 Overview
This repository contains **comprehensive open-access teaching materials** for **NGS-based pathogen surveillance and genomic epidemiology**, with **Rift Valley fever virus (RVFV)** as a real-world case study.
The materials integrate:
- 📊 **90-minute professional presentation** (38 slides, publication-ready figures)
- 📚 **25,000+ words of comprehensive documentation** (theory + practical workflows)
- 🧬 **Complete bioinformatics tutorials** (step-by-step, from SRA data to phylogenetics)
- 🎓 **Pedagogical framework** (learning objectives, assessment strategies, discussion prompts)
- 🛠️ **Practical tools guide** (Genome Detective, Nextstrain, SRA-Tools)
**Designed for**: Doctoral students, researchers, public health professionals, bioinformaticians entering genomic epidemiology.
---
## Why This Matters
### The Problem
- Emerging infectious disease outbreaks require rapid characterization
- Traditional diagnostics (cell culture) take 7–14 days
- Genomic surveillance can provide answers in 5–6 days
- **But**: Most researchers lack training in NGS-based outbreak genomics
### The Solution
This repository provides:
1. **Theoretical foundation** — understand the science
2. **Practical workflows** — use real tools on real data
3. **Best practices** — learn from published research
4. **Teaching resources** — deliver this material to others
### Real Impact
The methods covered here directly enabled:
- **Kenya 2021 RVF outbreak** — all 5 samples typed as Lineage C within weeks
- **Rapid public health response** — informed vector control and surveillance strategies
- **Lineage assignment tool** — now used globally (Genome Detective RVFV typing)
---
## What's Included
### 1. Presentation Materials (Ready to Deliver)
```
RVFV_NGS_Presentation_Final.pptx
├─ 38 professionally designe …