A library is often prepared by random fragmentation of DNA and ligation of common adaptor sequences. However, the generated short reads challenge the identification of structural variants, such as indels, translocations, and duplication. Large regions of simple repeats can further complicate the alignment. Alternatively, a jumping library can be used with NGS for the mapping of structural variation and scaffolding of de novo assemblies.
Jumping libraries can be categorized according to the length of the incorporated DNA fragments.