A method for sequencing a target double stranded polynucleotide molecule comprising the steps of: a) fragmenting one or more target double stranded polynucleotide molecules and using double stranded fragments thereof to generate a plurality of double stranded polynucleotide molecules, wherein each double stranded polynucleotide molecule comprises a first and second portion from the same fragment; b) ligating one adaptor to the 3' ends of the double stranded polynucleotide molecules created in step a) and ligating a different adaptor to the 5' ends of the double stranded polynucleotide molecules created in step a); c) attaching the plurality of double stranded polynucleotide molecules to a surface, wherein the surface is a patterned surface comprising two types of patches, wherein the first type of patch comprises a plurality of immobilized oligonucleotides complementary to the adaptor ligated to the 3' end of the double stranded polynucleotide molecules and a plurality of second oligonucleotides, and wherein the second type of patch comprises a plurality of the second oligonucleotides present on the first patch and a plurality of immobilized oligonucleotides complementary to the adaptor ligated to the 5' end of the double stranded polynucleotide molecules; and wherein the first portion of each of the polynucleotide molecules is attached to a location in the first type of patch on the surface and the second portion of each of the polynucleotide molecules is attached to a location in the second type of patch on the surface; d) separating the first and second portions of the polynucleotide molecules on the surface by contacting the molecules with a transposase to insert a transposon, thereby separating the first and second portions; e) amplifying the separated first and second portions of the polynucleotide molecules to produce a plurality of clusters on the surface; f) determining the sequences of the polynucleotide molecules in the clusters; g) comparing the sequence of polynucleotides in a first cluster to the sequence of polynucleotides in a second cluster and comparing the locations of the first and second clusters on the surface to determine whether the two polynucleotide sequences are located on the same target polynucleotide molecule, wherein the distance between the first and second clusters on the surface is positively correlated with the probability that the polynucleotides in the first and second clusters are from the same target polynucleotide molecule. a) fragmenting one or more target double stranded polynucleotide molecules and using double stranded fragments thereof to generate a plurality of double stranded polynucleotide molecules, wherein each double stranded polynucleotide molecule comprises a first and second portion from the same fragment; b) ligating one adaptor to the 3' ends of the double stranded polynucleotide molecules created in step a) and ligating a different adaptor to the 5' ends of the double stranded polynucleotide molecules created in step a); c) attaching the plurality of double stranded polynucleotide molecules to a surface, wherein the surface is a patterned surface comprising two types of patches, wherein the first type of patch comprises a plurality of immobilized oligonucleotides complementary to the adaptor ligated to the 3' end of the double stranded polynucleotide molecules and a plurality of second oligonucleotides, and wherein the second type of patch comprises a plurality of the second oligonucleotides present on the first patch and a plurality of immobilized oligonucleotides complementary to the adaptor ligated to the 5' end of the double stranded polynucleotide molecules; and wherein the first portion of each of the polynucleotide molecules is attached to a location in the first type of patch on the surface and the second portion of each of the polynucleotide molecules is attached to a location in the second type of patch on the surface; d) separating the first and second portions of the polynucleotide molecules on the surface by contacting the molecules with a transposase to insert a transposon, thereby separating the first and second portions; e) amplifying the separated first and second portions of the polynucleotide molecules to produce a plurality of clusters on the surface; f) determining the sequences of the polynucleotide molecules in the clusters; g) comparing the sequence of polynucleotides in a first cluster to the sequence of polynucleotides in a second cluster and comparing the locations of the first and second clusters on the surface to determine whether the two polynucleotide sequences are located on the same target polynucleotide molecule, wherein the distance between the first and second clusters on the surface is positively correlated with the probability that the polynucleotides in the first and second clusters are from the same target polynucleotide molecule.