The segments resulting from circularization during constructing jumping library are cleaved, and DNA fragments with markers will be enriched and subjected to paired-end sequencing.
These DNA fragments are sequenced from both ends and generate pairs of reads. The genomic distance between the reads in each pair is approximately known and used for the assembly process.
For example, a DNA clone generated by random fragmentation is about 200 bp, and a read from each end is around 180 bp, overlapping each other.
This should be distinguished from mate-pair sequencing, which is basically a combination of next generation sequencing with jumping libraries.