Compositions and methods for nucleic acid sequencing

A method of obtaining a sequence of an individual double-stranded nucleic acid template molecule, the method comprising:

• (a) fragmenting a nucleic acid sample, thereby providing a plurality of double-stranded nucleic acid molecules, said double-stranded nucleic acid molecules comprising (i) a first strand, and (ii) a second strand, which is complementary to the first strand;
• (b) ligating a hairpin loop to a first end of said double-stranded nucleic acid molecules to covalently link said first strand and said second strand at said first end of said double-stranded nucleic acid molecules, thereby producing a plurality of double-stranded nucleic acid template molecules, wherein said first strand and said second strand at said first end of each of said plurality of double-stranded nucleic acid template molecules is linked by said hairpin loop;
• (c) identifying individual nucleotides of said first strand and said second strand of an individual double-stranded nucleic acid template molecule from said plurality of double-stranded nucleic acid template molecules produced in step (b) using a real time, single-molecule sequencing process, said single-molecule sequencing process consisting of sequencing said individual double-stranded nucleic acid template molecule, thereby generating a single sequencing read from said individual double-stranded nucleic acid template molecule, wherein said single sequencing read comprises a first nucleotide sequence of said first strand and a second nucleotide sequence of said second strand;
• and
• (d) obtaining a sequence of said individual double-stranded nucleic acid template molecule by analyzing said single sequencing read using both said first nucleotide sequence of said first strand and said second nucleotide sequence of said second strand, which includes comparing the first nucleotide sequence and the second nucleotide sequence from said individual double-stranded nucleic acid template molecule.