In a short-jump library, 3 kb genomic DNA fragments are ligated with biotinylate ends and circularized. The circular segments are then sheared into small fragments and the biotinylated fragments are selected by affinity assay for paired-end sequencing.
There are two issues related to short-jump libraries. First, a read can pass through the biotinylated circularization junction and reduce the effective read length. Second, reads from non-jumped fragments (i.e. fragments without the circularization junction) are sequenced and reduce genomic coverage. It has been reported that non-jumped fragments range from 4% to 13%, depending on the size of selection. The first problem might be solved by shearing circles into a larger size and select for those larger fragments. The second problem can be addressed by using a custom barcoded jumping library.