The present disclosure provides methods for generating mate-pair libraries using a recombinase/recombination site system. The method allows for increased insert size, improved efficiency and simplicity of the steps involved, and improved data generation. Mate-pair libraries are helpful in providing positional information for the assembly of sequence data from short read sequencing platforms. The disclosure also embodies the mate-pair libraries as generated from these methods.
STATEMENT OF GOVERNMENTAL SUPPORT
 The invention described and claimed herein was supported by Contract No. DE-AC02-05CH11231 awarded by the U.S. Department of Energy under. The government has certain rights in the invention.