The invention provides methods for preparing DNA sequencing libraries for assembling short read sequencing data into longer contiguous sequences and providing for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes. The methods generally comprise incorporating adaptor or vector sequences into at least one member of a target fragment library, amplifying the population of target fragment library members to produce a plurality of copies of amplified DNA molecules, fragmenting the plurality of amplified DNA molecules, incorporating additional adaptor sequences, and amplifying a region of at least one of the plurality of amplified DNA molecules. At least one resulting amplicon comprises a sequence identical to or complementary to at least a portion of a sequence tag and a sequence identical to or complementary to a portion of a target fragment library member.