The current invention pertains to a method for sequencing of a target nucleic acid fragment from a nucleic acid sample, comprising the steps of cleaving the nucleic acid sample with a first and a second RNA guided or DNA guided endonuclease complex, preferably a first and a second gRNA-CAS complex, thereby generating the target nucleic acid fragment and at least one non-target nucleic acid fragment. The generated fragments are subsequently contacted with an exonuclease, wherein the exonuclease digests only the non-target nucleic acid fragments. Subsequently said target nucleic acid fragment is sequenced using nanopore selective sequencing. The invention further pertains to the use of the enriched target nucleic acid fragments for nanopore selective sequencing the target nucleic acid fragment.