Scaffolding
Mate pairs
Long mate paired libraries allow the sequencing of the two ends of a large insert. Nannochloropsis gaditana was sequenced with SOLiD Mate Paired libraries, one with average insert size of 2kbp, the other with an average insert size of 5kbp.
Mapping the mate pairs allows to:
- Verify the correctness of contigs, when both pairs map within the same contig
- Connect contigs, when both pairs map to different contigs
Correctness
The contig in the picture is shown with the physical coverage of mate paired libraries. The break in the coverage is due to the fact that the contig is a mis-assembly.
Physical coverage
The physical coverage is the number of time a sequence is covered by the two pairs, and the space between the two pairs.
Scaffolding
The mate paired reads connecting two contigs are shown in the picture. It’s important to check that the two pairs are mapped in the correct orientation and a reasonable distance. Below we depict a single mate paired pair, with the orientation of SOLiD and Illumina libraries:
Result
The whole scaffolding is a set of contigs placed in the correct reciprocal orientation.