3rd generation sequencing technologies such as Pacific Biosciences or Oxford Nanopore nowadays allow for the generation of extraordinary long reads (> 10 kb). This gives the opportunity for highly improved genome assemblies, e.g. completely closed bacterial genomes or eukaryotic genomes with high N50 values close to their final chromosome structure. At DSMZ a genome sequencing, assembly and annotation workflow has been developed within the last years to obtain a complete microbial genome including all replicons (e.g. plasmids and phages) within a few days. This allows for the first time for comparative genome studies on genome structure in order to conclude about genome stability in connection to the lifestyle of an organism.