The omnomicsQ application comes in two versions. The graphical user interface version can be operated manually, and the Linux version can be embedded into a NGS data analysis pipeline and operated automatically. Both run locally to ensure patient data privacy.

Each user organisation also has a dedicated omnomicsQ space on a cloud server. That space is used to store quality policies and calculated quality measures together with the sample descriptions. Once the local application has performed the quality checks, the quality values are moved to the cloud server together with a sample identifier. The user can access the quality information for all samples on the cloud server and download reports. User pipelines can have programmatic access via an application programming interface (API).