Patent ID: 7709197

Claim:
A method of characterizing nucleotide sequences of one or more target polynucleotides, said method comprising the steps of: (a) fragmenting said one or more target polynucleotides present in a predetermined coverage amount to form a population containing overlapping first-sized fragments having an average length less than those of said target polynucleotides; (b) forming a number of separate mixtures from said population of first-sized fragments, such number being selected such that a majority of first-sized fragments in each separate mixture is non-overlapping with every other first-sized fragment of the same mixture and such that the mixture of origin of each such first-sized fragment is determinable; (c) generating for each of said separate mixtures a plurality of target concatemers from said first-sized fragments, each target concatemer comprising multiple copies of at least a portion of a first-sized fragment; (d) disposing said target concatemers on a surface; and (e) generating a number of sequence reads from target concatemers of each of said separate mixtures, such sequence reads each having a length less than those of said first-sized fragments, and such numbers of sequence reads being selected such that said sequence reads of each separate mixture covers a majority of first-sized fragments therein, and providing complete or partial nucleotide sequences of said one or more target polynucleotides by ordering said sequence reads from said target concatemers.