This chapter outlines the key features of the tools and chemistries commonly used in routine workflows for second- and third-generation sequencing. Since genetic diagnostic technologies differ in several aspects, selecting the appropriate molecular setup—including reagents and NGS instruments—is essential to ensure the best possible outcome for patients. Each laboratory should carefully consider the distinctions between technologies designed for diagnostic use and those intended for translational or basic research, as these differences play a critical role in decisions about technological infrastructure. This section provides specific insights into the advantages and limitations of available commercial solutions, aiming to support laboratory professionals in selecting technologies that comply with national regulations. We hope this information will be helpful to readers.