Long-read sequencing technology provides great potential in several clinically relevant areas of human genomics. Recent advancements allowing increased sequencing throughput and accuracy at a more affordable cost have already been made. However, the applied workflows still contain bottlenecks, especially in the extraction process steps that increase variability in HMW DNA (50 kbp -250 kbp) yield and quality, while hindering the processing of higher sample numbers. Overcoming these hurdles by robust high-throughput, automated solutions will support the growing number of large-scale population genomics studies and clinical research applications.