Urek-d-2/aquavigil-wa

Pipeline WBE (Wastewater-Based Epidemiology) pour la surveillance épidémiologique au Togo — détection précoce des pathogènes dans les eaux usées # AquaVigil-WA 🌊 **Wastewater-Based Epidemiological Surveillance Pipeline for West Africa** *Pipeline de Surveillance Épidémiologique par Analyse des Eaux Usées — Togo, Afrique de l'Ouest* --- ## What is AquaVigil-WA? AquaVigil-WA is the **first open-source, sovereign, multi-pathogen WBE pipeline designed for West Africa**. By analyzing metagenomics data from wastewater samples collected at canals, open drains, and markets — environments without formal sewer networks — it detects epidemic signals **up to 2 weeks before hospitals are overwhelmed**. > **Target:** Cholera · Typhoid · Polio/Enterovirus · Antimicrobial Resistance (AMR) > **Pilot site:** Lomé, Togo — 5 sampling sites > **Goal:** Present operational results at CPHIA Addis-Ababa, November 2026 --- ## Why AquaVigil-WA vs Existing Programs? | Feature | Burkina Faso | Dakar/IPD | AquaVigil-WA | |---------|-------------|-----------|--------------| | In-country sequencing | ❌ (sent to Dakar) | ✅ | ✅ | | Public pipeline (GitHub) | ❌ | ❌ | ✅ | | Multi-pathogen (single sample) | ❌ | Partial | ✅ | | Non-sewered environments | ❌ | ❌ | ✅ | | Open data (PHA4GE compliant) | ❌ | ❌ | ✅ | | Real-time alerts (weekly) | ❌ (quarterly) | ✅ | ✅ | --- ## Pipeline Architecture ``` Terrain (M2 & M4) Qualité (M4) Brique 1 (M1) Prélèvement canaux/ ──▶ FastQC ──▶ Snakemake marchés/drains Trimmomatic Kraken2 .fastq brut MultiQC Bracken MiniKraken DB profil taxonomique Brique 2 (M3) Brique 3 (M1 & M3) Normalizer (PMMoV) ──▶ Dashboard FastAPI Trend Predictor Carte Leaflet.js ARIMA + IsolationForest API REST publique PHA4GE-compliant JSON Alertes SMS/email ``` --- ## Repository Structure ``` aquavigil-wa/ ├── workflow/ │ ├── Snakefile # Pipeline principal │ └── rules/ # Règles Snakemake modulaires │ ├── qc.smk # FastQC + Trimmo …