ENVIRONGEN (ENVIRONmental monitoring open GENomics toolkit) aims to deliver the first comprehensive, open, and validated bioinformatics toolkit for genomics-based environmental monitoring. While genomics surveillance is well established for clinical pathogens and antimicrobial resistance (AMR), no robust and interoperable solution currently exists for systematic analysis of environmental samples. ENVIRONGEN addresses this gap by developing a toolkit designed for broad scientific adoption.

The project focuses on detecting and characterizing viral pathogens and AMR determinants in environmental samples, using wastewater as a proof of concept. Building on Sciensano’s extensive expertise in pathogen genomics and surveillance, ENVIRONGEN extends genomics-based monitoring beyond clinical settings to support public health preparedness, early-warning systems, and environmental research.
 

ENVIRONGEN places strong emphasis on openness, quality, and long-term sustainability. The toolkit will be fully open-source, available via GitHub, and integrated into the Galaxy platform to ensure accessibility for both command-line users and researchers who prefer graphical interfaces.
 

This four-year project is funded by belspo. It is coordinated by Sciensano, with VIB/ELIXIR Belgium as a key partner responsible for integrating the toolkit into the Galaxy ecosystem.