Welcome to the advanced bioinformatics course on pathogen genomics, created by a collaboration between researchers from the Armauer Hansen Research Institute, the Institute of Tropical Medicine Antwerp and the University of Antwerp, and supported by the FA5 programme.

This is a continuation of the FA5 2025 introductory course and continues in its goals of supporting the implementation of sequencing bioinformatics to strengthen molecular surveillance and pathogen research. The course aims to provide an overview of key bioinformatics concepts related to pathogen genomics, followed by hands-on analysis of the participant’s own sequencing data. The course is divided into the following sections:

Acknowledgements

These materials were based on previous work by Pieter Moris (International Training Progamme - Fighting Malaria Across Borders - Bioinformatics Module - - licensed under CC BY 4.0) and the FA5 2025 introductory course (same team - licensed under CC BY 4.0).

The course was made possible by a cross-institute team of reseachers, listed above, and the FA5 programme.

About FA5: The Alliance for Education in Tropical Medicine and International Public Health, part of the FA5 agreement between ITM and the DGD (Directorate-General for Development Cooperation and Humanitarian Aid of the Belgian government), focuses on building educational partnerships and fostering collaboration with international higher education institutions in FA5 countries and beyond. Its main goal is to enhance quality, innovation, internationalization, and peer learning in postgraduate education, with mutual learning at its core. More info via this link.

Re-using these materials and how to cite us

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This (loosely-speaking) means that you are free to copy, redistribute or adapt any of the primary content on this website and in the git repository as you see fit, provided that you give us appropriate credit. Ideally, you do this by citing the Zenodo DOI (url to be included here after initial release). Please make sure to also provide proper attribution to the primary sources that we cite ourselves, whenever this is applicable.