Logical compartmentalization of automated library prep methods helps choosing which version of kits to use, when to run samples and when to stop at safe stopping points during the preparation of a library. For the construction of 96 sequencing-ready libraries with Illumina's Nextera DNA Flex kit in less than one day we recommend automated liquid handling systems with the possibility to program 4 methods and one off-deck incubation (figure 1). This allows to stop the library preparation after one of the steps if needed. This way the automated liquid handling system can accommodate different sample inputs (e.g., 24-plex or 96-plex) and provides full flexibility to match your busy day schedule.