Methods of amplifying and sequencing nucleic acids

A method for sequencing nucleic acids comprising:

• (a) fragmenting large template nucleic acid molecules to generate a plurality of fragmented nucleic acids;
• (b) delivering the fragmented nucleic acids into aqueous microreactors in a water-in-oil emulsion such that a plurality of aqueous microreactors comprise a single copy of a fragmented nucleic acid, a single bead capable of binding to the fragmented nucleic acid, and amplification reaction solution containing reagents necessary to perform nucleic acid amplification;
• (c) amplifying the fragmented nucleic acids in the microreactors to form amplified copies of said nucleic acids and binding the amplified copies to beads in the microreactors;
• (d) delivering the beads to an array of at least 10,000 reaction chambers on a planar surface, wherein a plurality of the reaction chambers comprise no more than a single nucleic acid bound bead;
• and
• (e) performing a sequencing reaction simultaneously on a plurality of the reaction chambers.