Patent ID: 8609341

Claim:
A method for sequencing a plurality of polynucleotides comprising: (a) binding a plurality of protection molecules to a plurality of polynucleotides; (b) cleaving polynucleotides in the plurality of polynucleotides that are bound to the protection molecules, thereby generating a plurality of polynucleotide fragments of substantially uniform size; (c) amplifying polynucleotide fragments of the plurality of polynucleotide fragments on a solid support, thereby producing an array of locations, each location comprising multiple copies of a single polynucleotide fragment of the plurality of polynucleotide fragments; and (d) performing paired-end sequencing on the copies of the polynucleotide fragments at a plurality of the locations of the array, wherein the paired end sequencing comprises sequencing a first strand of each of the copies, converting the first strand into a double-stranded template and sequencing a second strand of the double-stranded template.