Next generation sequencing produces an ever increasing amount of data, requiring increasingly fast computing infrastructures to keep up. We present GNATY, a collection of tools for NGS data analysis, aimed at optimizing parts of the sequence analysis process to reduce the hardware requirements. The tools are developed with efficiency in mind, using multithreading and other techniques to speed up the analysis. The architecture has been verified by implementing a variant caller based on the Varscan 2 variant calling model, achieving a speedup of nearly 18 times. Additionally, the flexibility of the algorithm is also demonstrated by applying it to coverage analysis. Compared to BEDtools 2 the same analysis results were found but in only half the time by GNATY. The speed increase allows for a faster data analysis and more flexibility to analyse the same sample using multiple settings. The software is freely available for non-commercial usage at http://gnaty.phenosystems.com/.