I'm learning about mate-pair sequencing and I don't really understand how does the process work. I understand the whole procedure of getting only the sequences that have the former DNA ends, but what happens next? What is the advantage of having a sequence built of fragments which were originally separated by several kilobases?
If you don't have a genome assembly... the mate pairs would help you in assembling a non-mate pair library by providing information about long-distance interactions. Any mate pairs that are sequenced are likely intra-chromosomal.
Also in situations with repeats you would get better resolution: