As of 2018, the Princess Máxima Center treats approximately 700 children with cancer (500 new cases, 200 relapses) per year. Exome sequencing and RNA sequencing will be performed as standard of care on all individuals and many patients are included in clinical studies and research cohorts, in which case whole genome sequencing will be performed. In both scenarios, primary patient material and research derived materials will be stored in a biobank and characterized at the molecular level by WES, WGS and RNA sequencing analyses. To keep track of sample relationships and analyses, a platform is needed which can store diverse sequencing data and sample metadata as well as support automated reproducible analyses. In essence ensuring that analyses are consistent and data is Findable, Accessible, Interoperable and Reusable. We have created a framework to both track the (meta) data of diagnostic as well as research applications and their analysis workflows. This shared infrastructure is based on a non-redundant small code base which is easy to maintain and guarantees analysis compatibility between diagnostics and research which is key for successful translational research and advanced patient care.