Preparing next generation sequencing libraries involves a multi-step process to fragment DNA, repair their ends, add adapters, and amplify the resulting DNA. This process, which involves multiple clean up steps in between, requires the user to frequently come back to the experiment between incubations. Automating this entire process in one protocol allows the user to step away from the bench to do other tasks. Here, we describe an automated protocol for the Opentrons Flex to prepare sequencing-ready libraries using the Twist Library Preparation Enzymatic Fragmentation (EF) Kit 2.0 and Twist Universal Adapter System.