The ThunderStorm™ system is a fully automated high-throughput targeted sequencing platform that enables researchers to determine all variations contained in any region of the genome. The ThunderStorm system supports a range of sequencing applications, including candidate gene screening, genome-wide association study follow up, deep sequencing of heterogeneous tumor samples, medical genetics, and targeted methylation analysis. The ThunderStorm is capable of simultaneously generating millions of unique droplet-based single molecule PCR reactions for targeting disease-specific loci. Walk-away capabilities allow for the automatic processing of up to 96 samples per run.