We are the first to show that high risk HPV TrDNA can be quantified with qPCR and Sequence-Capture assays and that high-risk HPV genomes can be assembled from TrDNA. We have developed qPCR and Sequence-Capture, Next-Generation Sequencing-based, HPV-Trans Renal DNA (TrDNA) assays to quantify high risk HPV DNA, which can be useful for cervical cancer screening. Our HPV TrDNA assay compares favorably in Specificity and Sensitivity to commercial HPV tests, making them an ideal alternative for low resource settings.