GenomicsForOneHealth

Pipelines & Team

Six domains, ten workflows

Reproducible nanopore workflows across One Health domains.

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

A metagenomic framework for rapid Listeria monocytogenes surveillance in food production environments

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

The team

Prof. Dr. Lara Urban

PI (Helmholtz AI & UZH)

Dr. Albert Perlas

Postdoc — Virome & AIV

Tim Reska

PhD — Metagenomics

Daniel Gygax

PhD — eDNA

Ela Sauerborn

PhD — CRE & Isolates

Harika Ürel

PhD — 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

Setup guide · Install & databases · Tools reference

Sequencing Advisor

What should I sequence with?

Describe your project and get a kit, basecalling model, and pipeline recommendation.

Sequencing advisor

Real-time Genomics for One Health