AMR Characterization Using Wastewater Metagenomics

Master's thesis research on antimicrobial resistance (AMR) characterization using wastewater metagenomic data.

📄 Core Documentation

Document	Purpose
Master Document	Single authoritative project reference
Analytical Pipeline	End-to-end methodology roadmap
Visualization Guide	Figure specifications & cleanup guidance
Decision Log	Methodological decisions with rationale

Quick Reference

Topic	Location
Research questions	Master Doc §3
Spatial gradient	Master Doc §5
Interpretation limits	Master Doc §7
Data sources	Master Doc §8
Pipeline workflow	Analytical Pipeline
Figure specifications	docs/figures/

Repository Structure

├── archive/            # Legacy/obsolete files
├── data/               # Metadata, datasets, processed results
│   └── metadata/       # Sample manifests, dataset registry
├── docs/               # Documentation
│   └── figures/        # Publication-quality figures
├── logs/               # Decision logs, progress tracking
├── pipeline/           # Bioinformatics and analysis code
├── Research Papers/    # Literature evidence base (29 papers)
├── requirements.txt    # Python dependencies
└── README.md           # This file

Project Status

Completed ✅

• Research Framework & One Health Positioning
• Tier-2 Inference Logic & Interpretation Boundaries
• Spatial Gradient Framework
• Dataset Identification & Curation Strategy
• Bioinformatics Pipeline Scaffolding
• Statistical Analysis Module
• Publication-Quality Figure Generation (6 figures)
• Comprehensive Documentation Suite

In Progress 🔄

• Metadata Enrichment (DRA runs via Entrez)
• Environment Setup (conda + bioinformatics tools)
• Pilot Analysis (subset of samples)

Planned 📋

• Full Dataset Processing
• Comparative Analysis & Diversity Metrics
• Result Synthesis & Interpretation
• Thesis Writing

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Last updated: 2026-01-30