Eurofins Genomics has developed long jumping distance (LJD) libraries for high throughput scaffolding of contigs. The LJD library is adapted to the Illumina HiSeq 2000 or the Illumina MiSeq 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:
1. Because of the differences in library generation the number of shotgun paired end reads is greatly reduced. Only about 1% of LJDs reads are shotgun paired-end reads.
2. 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. Hybrid 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.