The KAPA HyperCap Workflow v3 from Roche® combines the high conversion rate from KAPA HyperPrep or KAPA HyperPlus library preparation kits with the uniform target capture from the KAPA Target Enrichment kit to produce high-quality enriched NGS libraries. This workflow accommodates input of mechanically sheared gDNA (KAPA HyperPrep) or can use an upfront enzymatic fragmentation module for intact gDNA (KAPA HyperPlus). The KAPA HyperCap Workflow v3 automated on the Sciclone® G3 NGSx and iQ™ workstations has been demonstrated to reduce hands-on time, increase throughput processes and generate reproducible experimental data. Sequencing data of low-throughput and high-throughput sample processing reveals consistent target capture specificity and uniformity, with minimal PCR duplicates on both the Sciclone G3 NGSx and NGSx iQ workstations.