This practical course will detail Next Generation Sequencing (NGS) methodologies and how to analyse the sequence data to assemble de novo genomes or transcriptomes. The participants will learn how to perform quality control, trimming/filtering, and how to assemble short reads with various available software tools. They will also learn how to compare assemblies and how to annotate rapidly their draft assemblies. The last day is a minisymposium jointly organized by the Universities of Bern and Fribourg.