Plasmids are small, circular, extra-chromosomal genetic elements that, in bacterial pathogens, often harbor virulence or antibiotic resistance genes. Until recently, due to read length limitations in high-throughput sequencing technologies, it has been very challenging to retrieve plasmid information from genome assemblies. As a result, despite having good knowledge of virulence factors and antibiotic resistance genes and point mutations, our knowledge of plasmids - how they evolve, mutate and are shared between hosts - is still somewhat limited. With the advance of nanopore sequencing, it is now possible to routinely retrieve complete circular plasmid sequences from sequencing data. Therefore, a whole new set of possibilities for the analysis of plasmids has emerged. In this project we aim at building an automated pipeline for the identification, clustering, functional annotation and phylogeny of plasmids. The project should result in a reproducible, open-source workflow, which will be published in an scientific journal. The resulting workflow will also be used publicly available assemblies of different species of Enterobacter, which should lead to the discovery of novel plasmids, as well as evolutionary insights, and and hopefully new perspective into the mutaional landscape of plasmid-born resistance genes in bacterial pathogens. While software development for this project can to a large extent happen on a laptop, some steps of the pipeline will require larger computing resources, mainly for testing scalability, and benchmark tools in situations closer to real-world use. (This storage project depends on the small compute proposal NAISS 2023/23-626)