The assembly process assembles single overlapping reads to larger contigs. In the first instance, the contigs are not ordered. Scaffolding means to determine the order and orientation of the contigs. It can be achieved for example by sequencing long jumping distance libraries on the Illumina instruments. This technology creates pairs of short sequence tags, which are originally positioned 3 kbp, 8 kbp, 20 kbp or 40 kbp apart from each other.
Scaffolding matches the paired ends to the contigs under consideration of the original distance and thereby brings the contigs into order.