This application note showcases the Twist FlexPrep UHT Library Preparation and Hybridization Kit using bovine samples from ear punches. We provide guidance for gDNA extraction and a comparison to ground truth PCR-free whole genome sequencing (WGS). Libraries generated with Twist FlexPrep UHT Library Preparation Kit have high concordance to the ground truth datasets, demonstrating similar data quality to microarrays. By combining this kit with custom target enrichment (TE) panels, users are able to easily identify and investigate novel regions of interest that can impact population management and breeding choices.