we described a method of mate-pair library construction by controlling DNA polymerization with nick translation and primer extension. Compared with reported approaches, our approach can increase circularization efficiency by 8-fold and extremely eliminate read-pairs not crossing the circularization junction (39.3-fold change), resulting in an approximately 50% of increment of physical coverage when with the same number of read-pairs. In addition, the reagent cost for this approach has 88.6% reduction, whereas the minimum requirement of DNA input is only 1 μg. Furthermore, the feasibility of sequencing platform neutral has been demonstrated with data from four sequencing platforms. Overall, our approach advances the application of low-pass whole-genome sequencing in a clinical setting.