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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.
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