This research presents a genetic variant discovery SoC for analyzing Next-generation sequencing data which is embedded with the processorconnected with some peripherals. With hardware-optimized algorithm sBWT, we greatly speed up the process of short reads mapping by k-ordered FM-indexsuffix grouping. After short reads mapping, we utilized de bruijn graph for sequence assembly to rebuild haplotypes,built haplotypes are compared to the reference genome to detect genome variations. The detected variations are written to files for further clinical diagnosisresearch analysis.