A method of sequencing a target nucleic acid, comprising: a) providing a plurality of substrates, wherein said plurality of substrates is n, each substrate of said plurality of substrates is designed as a different substrate (i), wherein said (i) is an integer from 1 to n, wherein each different substrate of said plurality of substrates comprises a capture site comprising a capture probe, and wherein said capture probe comprises a sequence that is complementary to a portion of said target nucleic acid, wherein said target nucleic acid comprises a fragment of a source nucleic acid; b) forming a hybridization complex on each of said different substrates (i), wherein said hybridization complex comprises said capture probe and said target nucleic acid, wherein said capture probe is hybridized to said portion of said target nucleic acid; c) extending said capture probe in said hybridization complex on each of said different substrates (i) by repeating i-1 times the step of: contacting said hybridization complex on each of said different substrates (i) sequentially with 1) one of native dATP, dCTP, dGTP and dTTP; or 2) a mixture of two or three native dNTPs followed by one or more rounds of two or more different native dNTPs until all four native dNTPs are added at least once, in the presence of a polymerase, thereby extending said capture probe in said hybridization complex by one or more bases using said target nucleic acid in said hybridization complex as template, wherein said extending said capture probe in said hybridization complex occurs in a separate extension reaction for each of said different substrates (i); d) further extending said capture probe in said hybridization complex on each of said different substrate (i) sequentially with one of labeled dATP, dCTP, dGTP and dTTP in the presence of a polymerase; e) detecting incorporation of said labeled dATP, dCTP, dGTP and dTTP in said hybridization complex on each of said different substrates (i), thereby obtaining a sequence read from said hybridization complex on each of said different substrates (i); and f) determining a nucleotide sequence of said target nucleic acid by assembling said sequence reads, wherein said assembling is performed on a computer. a) providing a plurality of substrates, wherein said plurality of substrates is n, each substrate of said plurality of substrates is designed as a different substrate (i), wherein said (i) is an integer from 1 to n, wherein each different substrate of said plurality of substrates comprises a capture site comprising a capture probe, and wherein said capture probe comprises a sequence that is complementary to a portion of said target nucleic acid, wherein said target nucleic acid comprises a fragment of a source nucleic acid; b) forming a hybridization complex on each of said different substrates (i), wherein said hybridization complex comprises said capture probe and said target nucleic acid, wherein said capture probe is hybridized to said portion of said target nucleic acid; c) extending said capture probe in said hybridization complex on each of said different substrates (i) by repeating i-1 times the step of: contacting said hybridization complex on each of said different substrates (i) sequentially with 1) one of native dATP, dCTP, dGTP and dTTP; or 2) a mixture of two or three native dNTPs followed by one or more rounds of two or more different native dNTPs until all four native dNTPs are added at least once, in the presence of a polymerase, thereby extending said capture probe in said hybridization complex by one or more bases using said target nucleic acid in said hybridization complex as template, wherein said extending said capture probe in said hybridization complex occurs in a separate extension reaction for each of said different substrates (i); d) further extending said capture probe in said hybridization complex on each of said different substrate (i) sequentially with one of labeled dATP, dCTP, dGTP and dTTP in the presence of a polymerase; e) detecting incorporation of said labeled dATP, dCTP, dGTP and dTTP in said hybridization complex on each of said different substrates (i), thereby obtaining a sequence read from said hybridization complex on each of said different substrates (i); and f) determining a nucleotide sequence of said target nucleic acid by assembling said sequence reads, wherein said assembling is performed on a computer.