A method, comprising: a) providing; i) a first forked end adapter comprising a first duplex DNA sequence, wherein said first duplex DNA sequence comprises a first nucleic acid sequence ligated to a first primer sequence and a second nucleic acid sequence ligated to a second primer binding sequence; ii) a second forked end adapter comprising a second duplex DNA sequence, wherein said second duplex DNA sequence comprises a third nucleic acid sequence ligated to third primer sequence and a fourth nucleic acid sequence ligated to a fourth primer binding sequence; iii) a genomic DNA fragment capable of ligating said first duplex DNA sequence to said second duplex DNA sequence; iv) a second primer capable of binding to said second primer binding sequence; v) a fourth primer capable of binding to said fourth primer binding sequence; and vi) a bead comprising a first primer and a third primer, wherein said first and third primers are attached at the 5' end; b) contacting said genomic DNA fragment with said first forked end adapter and said second forked end adapter wherein said genomic DNA fragment ligates between said first duplex sequence and said second duplex sequence, thereby forming a ligated forked end adapter primer pair; and c) emulsion amplifying said ligated forked end adapter primer pair with said bead, said second primer and said fourth primer, thereby co-localizing a first double stranded bead product and a second double stranded bead product on said bead; wherein said first primer sequence and said second primer binding sequence of the first forked end adapter are different from said third primer sequence and said fourth primer binding sequence of the second forked end adapter. a) providing; i) a first forked end adapter comprising a first duplex DNA sequence, wherein said first duplex DNA sequence comprises a first nucleic acid sequence ligated to a first primer sequence and a second nucleic acid sequence ligated to a second primer binding sequence; ii) a second forked end adapter comprising a second duplex DNA sequence, wherein said second duplex DNA sequence comprises a third nucleic acid sequence ligated to third primer sequence and a fourth nucleic acid sequence ligated to a fourth primer binding sequence; iii) a genomic DNA fragment capable of ligating said first duplex DNA sequence to said second duplex DNA sequence; iv) a second primer capable of binding to said second primer binding sequence; v) a fourth primer capable of binding to said fourth primer binding sequence; and vi) a bead comprising a first primer and a third primer, wherein said first and third primers are attached at the 5' end; i) a first forked end adapter comprising a first duplex DNA sequence, wherein said first duplex DNA sequence comprises a first nucleic acid sequence ligated to a first primer sequence and a second nucleic acid sequence ligated to a second primer binding sequence; ii) a second forked end adapter comprising a second duplex DNA sequence, wherein said second duplex DNA sequence comprises a third nucleic acid sequence ligated to third primer sequence and a fourth nucleic acid sequence ligated to a fourth primer binding sequence; iii) a genomic DNA fragment capable of ligating said first duplex DNA sequence to said second duplex DNA sequence; iv) a second primer capable of binding to said second primer binding sequence; v) a fourth primer capable of binding to said fourth primer binding sequence; and vi) a bead comprising a first primer and a third primer, wherein said first and third primers are attached at the 5' end; b) contacting said genomic DNA fragment with said first forked end adapter and said second forked end adapter wherein said genomic DNA fragment ligates between said first duplex sequence and said second duplex sequence, thereby forming a ligated forked end adapter primer pair; and c) emulsion amplifying said ligated forked end adapter primer pair with said bead, said second primer and said fourth primer, thereby co-localizing a first double stranded bead product and a second double stranded bead product on said bead;