Next generation sequencing (NGS) requires a sophisticated level of bioinformatic evaluation procedures to handle and analyze the vast amount of sequencing data. NGS together with profound bioinformatical knowledge enables scientists to seek answers to diverse biological questions. Therefore, both standardized and customized methods were integrated and developed for the downstream analysis of sequencing data. They are are provided on a highly interactive analysis platform, which provides easy web access to sequencing data analysis – without prior bioinformatical knowledge – for our collaboration partners. The large calculations required by NGS are processed in a high-performance computing environment. Currently, the computational cluster comprises a mirrored 110 TB server, 152 cores and 877 GB RAM. Thus, results are received in a timely manner.