The European Society of Clinical Microbiology and Infectious Diseases (ESCMID) workshop on genomics and metagenomics was held in Lausanne from 9th to 12th September 2019. As many as 68 participants from 20 countries from all 5 continents participated to this postgraduate technical workshop. During 4 days, the participants shared their time between conferences on various topics related to the implementation of genomics and metagenomics in a clinical diagnostic laboratory. These included talks from the clinics and talks from bioinformatic experts. A significant time was also dedicated to practicals covering various aspects of the data analysis of NGS sequences (quality check, annotation of virulence and antibiotic resistance genes, taxonomic assignment of amplicons, strain typing, …). This ESCMID meeting co-organized by A Lebrand and G Greub, with the help of the European Study Group for Genomics ad Molecular Diagnostics (ESGMD) provided a unique opportunity to exchange knowledge and ideas on the most recent bioinformatic approaches, as well as how to report such NGS results in diagnostic laboratories. This meeting report summarizes the key messages of this meeting.