Eurofins MWG Operon has developed long jumping distance (LJD) libraries for high throughput scaffolding of contigs. Like the Illumina mate-pair library the LJD library is adapted to the Illumina HiSeq 2000 technology. While the mate-pair library displays jumping distances of 2 kbp to 5 kbp, LJD libraries do show much more precise distances, thus improving assembly quality. LJD libraries are being offered for 3kbp, 8 kbp, 20 kbp and even 40 kbp jumping distance.

In addition, other advantages argue for the LJD library: First, because of the differences in library generation, portion of inward-facing reads (see explanation in the mate-pair FAQ) is greatly reduced. Second, within the LJD library the sequences from one and the other end of the original fragment (3 kbp, 8 kbp, 20kbp or 40 kbp) are separated by an adaptor sequence. Chimeric reads, as present in mate-pair libraries (see explanation in the mate-pair FAQ) are therefore almost completely eliminated when using LJD libraries. The changeover is defined by the presence of the adaptor.