In comparison to traditional paired-end DNA sequencing, mate-pair sequencing allows the generation of long-insert paired-end DNA libraries. These are especially useful for applications, such as de novo sequencing, genome finishing, structural variation detection or the identification of complex genomic rearrangements.

For mate-pair sequencing DNA is fragmented into 2-5 kb fragments, the ends are repaired with biotin labeled dNTPs. The labeled fragments are then circularized and fragmented again into 400 - 600 bp pieces. Fragments with the biotin label are then captured, enriched, end-repaired, ligated with adapters and finally sequenced. The resulting reads have insert sizes in the range of 2-5 kb.

In combination with traditional paired-end sequencing this method provides a comprehensive set of reads for complex genomic applications.