New high-throughput sequencers are able to produce data at an unprecedented scale while sequencing costs are in free fall. Primary sequence data management involves an unavoidable step of quality control and pre-processing and is computationally expensive. There are some solutions available to carry out a quality control check, however they are slow and the report is based only in the partial analysis of the data. We present a High Performance Computing (HPC) solution for quality control check of the widely used standard FASTQ that identifies and exploits the hardware (CPUs and GPUs) available in the computer in which it is running. This solution outperforms 5x any conventional solution based on CPU processors. Moreover, the QC is exhaustive and it also carries out several preprocessing steps on the data.