matepair

Mate-pair sequencing is a library preparation and sequencing approach that generates read pairs from the distal ends of relatively large DNA fragments. Compared with standard paired-end sequencing, which reads both ends of short fragments, mate-pair protocols provide long-range genomic information by linking ends of large inserts, aiding assembly and structural variation analysis.

The typical workflow starts with high-molecular-weight DNA. Fragments of a defined size range, often 2–10 kilobases (with some protocols extending to 20–40 kb), are circularized so that the fragment ends become adjacent. The junctions are biotinylated, and the circular molecules are sheared into smaller pieces. Fragments containing the junction are enriched and prepared for sequencing, yielding read1 and read2 that originate from the ends of the original large fragment. The resulting read pairs are oriented outward, reflecting their ends located at opposite sides of the fragment.

Mate-pair data are especially useful for de novo genome assembly and scaffolding, where long-range linkage helps connect contigs across repetitive regions and improve contiguity. They also support the detection of structural variations, such as insertions, deletions, inversions, and translocations, when analyzed with appropriate software and in combination with other data types.

Limitations include more complex and less robust library preparation, higher potential for chimeric reads, and the need for specialized computational pipelines to handle large inserts and outward-oriented reads. As sequencing technologies advance, long-read approaches and chromosome conformation methods (such as Hi-C) increasingly complement or replace mate-pair strategies for obtaining long-range genomic information.