This course aims at providing participants with the essential tools to understand the output of bioinformatics analysis pipelines, interpret the results for making better-informed clinical recommendations, recognise the main challenges and limitations when using NGS bioinformatics analysis pipelines in clinical settings, and acquire a common language to foster multidisciplinary discussions of results with clinical bioinformaticians in their team. It will cover the essential bioinformatics concepts on NGS data management and processing for typing and phylogenetics, resistance and virulence prediction, and metagenomics-based taxonomic classification.