Pandemics (2024 Sept)

Vir-o-matic

By Heba Farookhi (Published on January 27, 2025)

This project was a runner-up for the "Build a thing" prize on our Pandemics (Sept 2024) course. The text below is an excerpt from the final project.

Background and Context

Effective pandemic preparedness and response require robust tools for early detection and monitoring of emerging pathogens. Wastewater-based epidemiology (WBE) has proven to be a powerful approach for tracking community-level infections, offering a non-invasive, cost-effective method for surveillance of pathogens, including viruses. By analyzing urban sewage samples, researchers can detect circulating viral pathogens before clinical cases surge, providing an early warning system for potential outbreaks.

Objective

This project presents a Google Colab-based metagenomic analysis pipeline designed to detect and characterize known and novel viruses from wastewater samples. The pipeline leverages popular bioinformatics tools such as FastQC, fastp, Kraken2 (with a viral-only database), Krona, MEGAHIT, and VirSorter2, all orchestrated using Nextflow for reproducibility and scalability. The primary goal is to create an accessible, user-friendly tool that enables researchers, public health labs, and biosecurity professionals to perform rapid and reliable viral analyses during pandemics or other public health emergencies.

Full project

You can view the full project here.