Galaxy@Sciensano is a Galaxy server dedicated completely towards public health applications. The instance focuses on making available tools, pipelines and databases relevant for using whole genome sequencing for routine pathogen typing and characterization, and outbreak detection, in an applied public health setting. Upon registration, this Galaxy server is freely accessible for academic and non-profit usage.

The main goal of this Galaxy instance is to serve as an ‘all-in-one’ portal for microbial public health applications. The application incorporates many of the standard tools available in the Galaxy Toolshed. Of particular interest are the in-house tools, pipelines and databases that have been developed and deployed into this Galaxy server making it a hybrid mix of general bioinformatics tools combined with many specialized additions. The majority of the in-house developed tools provide entire solutions that perform all required steps, without the need to go through all individual steps of the next generation sequencing data analysis process.


A series of training videos on how to use the application are available on YouTube. The introduction videos are accompanied with tutorials on the basics of next-generation sequencing data analysis and more specialized topics of interest in public health.