As a result of the rapid evolution of biotechnology in recent years, next-generation, high throughput sequencing methods have been introduced. Competition between sequencing technology companies has resulted in drastically declining prices. Thus the amount of data generated by next-generation sequencing instruments has been increasing exponentially, therefore processing data is a serious challenge. The main task is the detection and biological interpretation of genetic variations. The correct interpretation and annotation of these variations creates the opportunity to acquire genome-scale biological knowledge. This knowledge can be utilized in many ways, e. g. in personal medicine and environmental protection.