Long-range sequence assembly in whole-genome shotgun sequencing

Individual sequence reads generated in a whole-genome shotgun-sequencing project are initially assembled into sequence contigs. Groups of sequence contigs are then organized into scaffolds on the basis of linking information provided by read pairs (in each case, with one sequence read from a pair assembling into one contig and the other read into another contig). In turn, the scaffolds can be aligned relative to the source genome (represented by an encyclopedia set) by the identification of already mapped, sequence-based landmarks (e.g., STSs, genetic markers, genes; depicted as red circles) in the sequence contigs, thereby associating them with a known location on the genome map.