GenomicsForOneHealth

Real-time Genomics for One Health

Using nanopore technology and AI, we develop genomic surveillance strategies at the intersection of human, animal, and environmental health — empowering our understanding of pathogens, their transmission, drug resistance, and virulence in the context of food safety, water and air quality, and clinical monitoring.

Urban Lab  ·  Pipeline Advisor

Pipelines

10 workflows across 6 One Health domains

Based at

University of Zurich — Food Safety & One Health Institutes

Funded by

EU Horizon Europe, Helmholtz Association, UKRI, and others

Our Pipelines

Six domains, ten workflows

Each pipeline is a self-contained, reproducible workflow built on nanopore long-read sequencing. Click through to the documentation and source code for each.

Environmental Metagenomics

Air & Wetland

Nanopore metagenomics for bioaerosol communities and wetland pathogen & AMR surveillance.

Air pipeline · Wetland pipeline

eDNA Metabarcoding

Zambia Biodiversity

Portable nanopore eDNA metabarcoding for vertebrate biodiversity monitoring in remote field conditions.

eDNA pipeline

Food Safety

Listeria Adaptive Sampling

High-resolution genomic analysis of Listeria monocytogenes from complex food matrices using adaptive sampling.

Listeria pipeline

Clinical Isolates & Plasmid Profiling

AMR, CRE & Host Association

Rapid clinical AMR detection, CRE plasmid clustering, and methylation-based resistance–pathogen linkage.

AMR · CRE · AMR-Host

Veterinary & Zoonotic Surveillance

Avian Influenza & Transmission

Rapid AIV profiling from DNA and RNA nanopore data, plus variant calling for cross-host transmission tracking.

AIV profiling · Feather to Fur

Viability Assessment

Squiggle4Viability

Deep learning on raw nanopore signals to distinguish viable from dead microorganisms without culture.

Squiggle pipeline

Highlighted Publication

Real-time genomics for One Health

Urban, Perlas, Francino, Martí-Carreras, Muga, Mwangi, Boykin Okalebo, Stanton, Black, Waipara, Fontsere, Eccles, Ürel, Reska, Morales, Palmada-Flores, Marques-Bonet, Watsa, Libke, Erkenswick, van Oosterhout

Molecular Systems Biology, 2023

Read the paper

Our Team

The One Health group

Prof. Dr. Lara Urban

Principal Investigator (Helmholtz AI & University of Zurich)

Dr. Albert Perlas

Former Postdoc — Virome & Avian Influenza

Tim Reska

PhD Student — Metagenomics (Air & Wetland)

Daniel Gygax

PhD Student — eDNA Metabarcoding

Ela Sauerborn

PhD Student — CRE Plasmid & Isolates

Harika Ürel

PhD Student — Plasmid & Viability

Getting Started

Clone and run

git clone https://github.com/ttmgr/GenomicsForOneHealth.git
cd GenomicsForOneHealth
mamba env create -f environment.yaml
conda activate genomics-onehealth

See the full setup guide, install & databases, and tools reference for details.

Bonus Tool

Pipeline Advisor

Answer a few questions about your sequencing project. The advisor will recommend a kit, basecalling model, and analysis pipeline — with rationale, protocol links, and ready-to-run commands.

Sequencing advisor

Describe your project