High-throughput next-generation sequencing (NGS) workflows are required for population-level genomic research that aid SNP detection and discovery for genetic verification, breeding, and microbiome analysis. The cost and effort required in processing individual samples remain a barrier to efficient NGS library preparation. We present innovative and automation-friendly technologies that reduce cost and time: Normalization by LigationTM (NBL) and library preparation multiplexing with inline barcodes. We perform experiments using our high-throughput workflow on real-life bovine samples and demonstrate concordance of SNP detection with ground truth datasets.