These are called U-unitigs. The next phase is called scaffolding. This is analogous to setting up the frame of a building. A contiguous sequence of ordered unitigs is a contig. During scaffolding, the assembler orients contigs using mates.
Most mate pairs are reliable landmarks-they stick together and remain the same distance apart.
Sets of contigs that are ordered and oriented using enforcing pairs are called scaffolds. At this point, the scaffolding is continuous except for gaps. Other gaps contain repetitive sequence that can now be closed using the unitigs that were set aside earlier by the discriminating statistic. Rocks must be linked to the contigs on either side of a gap by two or more mates. Stones are linked to the contigs by only one mate.