We do not recommend using most commercially available enzymatically based DNA fragmentation mixes in the E5hmC-seq workflow, as enzyme-based shearing processes may affect methylation marks on the DNA. However, NEBNext UltraShear™ (NEB #M7634) has been specifically designed to fragment DNA and retain methylation marks. For specific recommendations on pairing NEBNext UltraShear with NEBNext® E5hmC-seq please contact NEB Technical Support.