Next-generation sequencing (NGS) has been increasingly used in a wide range of research communities and in routine clinical practice and leads to an ever increasing amount of sequencing data. Sequencing data comes with, several challenges such as sharing, storing, integrating, analyzing, and interpretion. The management of the expanding amount of data is challenging and, especially for human omics data, privacy protection is crucial. Unraveling the causes of rare diseases is critically dependent on data sharing, but progress is hampered by regulations and privacy concerns. To overcome the concerns associated with centralized human genomic data storage, we developed a federated analysis platform, referred to as Widely Integrated NGS (WiNGS). The presented approach enables datasharing and combined data-analysis of omics data across a consortium without a centralized data store. Moreover, the platform incorporates extensive variant interpretation tools from genotype to phenotype for the diagnosis of rare developmental disorders.