The immune system’s Human Leukocyte Antigen I (HLA) locus has the highest genetic diversity in the human genome. Due to the great similarity between highly polymorphic alleles in the HLA region, its extreme variability and complex structure, it has been difficult to align and phase haplotypes of HLA to standard linear reference genomes using short-read sequencing. In collaboration with Twist Biosciences, we developed a high-throughput, one-step fragmentation and barcoding method to capture and prepare DNA suitable for long-read targeted sequencing and test its performance using samples of diverse ancestries from the Human PanGenome project and the International Histocompatibility Working Group.