SUMMARY: Recent advances in single-cell sequencing made it possible to not just analyze a cell's individual expression pattern, but to gain insights into a single cell's genome using the cutting-edge technology single-cell DNA sequencing. Mission Bio is, with the Tapestri platform, one of the few providers of this technology. So far, however, there is only little open-source software available for user-friendly processing and quality analysis of this data type. With scafari, we present a tool that offers easy-to-use data quality control as well as explorative variant analyses and visualization. AVAILABILITY AND IMPLEMENTATION: scafari is implemented as an R Bioconductor package featuring a shiny application and is available at https://bioconductor.org/packages/scafari.