There are over 400 million formalin-fixed paraffin-embedded (FFPE) tissue samples archived in biobanks worldwide. These diseased and normal tissue collections are valuable resources for molecular genetic studies. However, the challenges of DNA extraction from FFPE tissues, including formaldehyde cross-linking, degradation, and mixtures of single-stranded and double-stranded DNA, result in low yields of usable material for downstream assays. Hence, quality control of samples is critical prior to costly experiments, such as next generation sequencing. On-chip and automated electrophoretic devices were evaluated for the characterization of FFPE and fresh-frozen DNA samples prior to and during target-enrichment and next generation sequencing workflows.