Paired-end reads from a library of 2-kb fragments cannot fill a 10-kb gap. In this method the idea was to find the pair-end reads to span the gaps between two sequence contigs.
Similarly, paired-end reads can be used to join two sequence contigs into a single ordered and oriented scaffold. Library of circularized genomic DNA fragments of desired sizes are formed.
On circularization forms for short segments of previously distant sequences located at the ends of each fragment to be juxtaposed on either side of a linker sequence. Shearing of the circular molecules, amplification, and sequencing of linker-containing fragments produces paired end reads. They are equivalent to those obtained, for sequencing of traditional library inserts.
In contrast, if one end of an insert was part of one contig and the other was part of a second contig, then the insert must span the gap between two contigs. Moreover, the two contigs were clearly near each other because, the size of the clone is known as it comes from a library of genomic inserts of uniform size.
The sizes may be 2 kb, 100 kb, or 150 kb or more. The distance between the end reads was known. In this manner, the distance between the end reads automatically determines the relative orientation of the two contigs.
Thus, the gapped collections of joined together sequence cotigs are called as scaffolds.