1. A method of polynucleotide sequencing, comprising: (a) providing a plurality of populations of target polynucleotide fragments, each of the target polynucleotide fragments having an internal nucleotide sequence and two ends, each of the target polynucleotide fragments being inserted into a circular vector; (b) cleaving the internal nucleotide sequence of each of the target polynucleotide fragments thereby removing the internal nucleotide sequence of each of the target polynucleotide fragments and leaving a segment of each end of the target polynucleotide fragments in the vector; and (c) determining the nucleotide sequences of the segment of each end of the target polynucleotide fragments in the vector after the cleaving step.