DNA and Library Preparation Methods for Whole-Genome Sequencing

This technical report evaluates various DNA extraction and library preparation methods for whole-genome sequencing (WGS) of bacterial pathogens, specifically focusing on their efficiency and cost-effectiveness. The study compares four DNA extraction methods, including automated nucleic acid extraction and two rapid lysis techniques, heat shock lysis and glass bead disruption. Additionally, four library preparation kits are assessed for their performance on three bacterial species: Bacillus cereus, Staphylococcus epidermidis, and Enterobacter cloacae. Key performance indicators such as sequencing depth, genome assembly quality, and GC bias are analyzed to determine the optimal combination of methods. Results indicate that the choice of DNA extraction and library preparation significantly impacts WGS quality, with glass bead disruption proving effective across all species tested. The findings underscore the importance of method selection based on bacterial characteristics to achieve high-quality sequencing outcomes, which is crucial for clinical diagnostics and public health applications.