Patent ID: 6942975

Claim:
A method of creating a genomic sequence scaffold, the method comprising the steps of: a) generating a plurality of fasteners, wherein said fasteners are sequence reads that span both the left and right sides of a restriction endonuclease site; b) generating a plurality of straddles, wherein said straddles are pairs of sequence reads that are separated by at least about 10 kb and wherein one sequence read of the pair is to the left of a restriction endonuclease site and the other sequence read of the pair is to the right of another restriction endonuclcase site; and c) anchoring straddles to fasteners, wherein said anchoring comprises aligning sequence reads of straddles to sequence reads of fasteners, thereby connecting straddles in instances where a straddle comprises a sequence read that aligns to one side of a restriction endonuclease site spanned by a fastener, and another straddle comprises a sequence read that aligns to the other side of the same restriction endonuclocase site.