Mate pair methods were developed to help produce novel genome assemblies. They enable two DNA fragments that are originally separated by 1-20 kB to be sequenced, working around the tech limitations of short next generation sequencing reads. Knowledge of the distance between these two DNA fragments helps in de novo sequencing where structural variant detection and the identification of rearrangements are important. The combination of mate pair along with shorter paired-end reads maximizes sequencing coverage across repetitive regions and aids in closing contigs and scaffolds into a cohesive genome map.
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The Nextera Mate Pair Kit has been optimized for use with 1 - 4 µg of genomic DNA and is designed for the construction of libraries for the purposes of de novo assembly of small genomes, genome finishing and detection of structural variations (SVs). After enzymatic fragmentation and adapter tagging (tagmentation), a distribution of fragments with an average insert size of 5kb are generated. Smaller sized fragments circularize more efficiently than larger fragments. After circularization, linear DNA is digested and circularized DNA is sheared. After a cleanup step, a DNA-Seq protocol is followed using a “with bead” approach which reduces the amount of material lost during transfer steps.