A method of identifying sequences that are derived from paired strands of a double-stranded nucleic acid fragment, the method comprising: dissolving a plurality of double-stranded, biologically-derived nucleic acid fragments into an aqueous solution; dissolving into the same aqueous solution a plurality of synthetic dilute template oligonucleotide molecules, wherein DTO molecules comprise a degenerate tag sequence incorporated within a primer sequence; distributing the solution into a plurality of compartments, wherein a compartment is unlikely to contain two or more double-stranded, biologically-derived nucleic acid fragments whose amplification products align to the same genomic reference sequence; copying and amplifying both strands of the compartmentalized double-stranded, biologically-derived nucleic acid fragments by performing PCR, producing biologically-derived DNA copies; simultaneously copying and amplifying the compartmentalized DTO molecules by PCR, producing within each compartment a plurality of clonal DTO copies comprising compartment-specific tags; attaching one or more compartment-specific DNA sequence tags to the amplified biologically-derived DNA copies by PCR using the clonal DTO copies as primers, resulting in the same tag or set of tags being attached to copies of both strands of a double-stranded, biologically-derived nucleic acid fragment; combining the compartments containing amplified tagged DNA copies; sequencing all or a subset of the amplified tagged DNA copies; and identifying sequences that are derived from paired strands of a double-stranded, biologically-derived nucleic acid fragment based on sharing of a common compartment-specific DNA sequence tag or set of tags. dissolving a plurality of double-stranded, biologically-derived nucleic acid fragments into an aqueous solution; dissolving into the same aqueous solution a plurality of synthetic dilute template oligonucleotide molecules, wherein DTO molecules comprise a degenerate tag sequence incorporated within a primer sequence; distributing the solution into a plurality of compartments, wherein a compartment is unlikely to contain two or more double-stranded, biologically-derived nucleic acid fragments whose amplification products align to the same genomic reference sequence; copying and amplifying both strands of the compartmentalized double-stranded, biologically-derived nucleic acid fragments by performing PCR, producing biologically-derived DNA copies; simultaneously copying and amplifying the compartmentalized DTO molecules by PCR, producing within each compartment a plurality of clonal DTO copies comprising compartment-specific tags; attaching one or more compartment-specific DNA sequence tags to the amplified biologically-derived DNA copies by PCR using the clonal DTO copies as primers, resulting in the same tag or set of tags being attached to copies of both strands of a double-stranded, biologically-derived nucleic acid fragment; combining the compartments containing amplified tagged DNA copies; sequencing all or a subset of the amplified tagged DNA copies; and identifying sequences that are derived from paired strands of a double-stranded, biologically-derived nucleic acid fragment based on sharing of a common compartment-specific DNA sequence tag or set of tags.