I find myself confused about insert size and pairing of reads. How are read pairs paired? As in, how does the aligning software know that they belong together? How does the sequencing machine? And, will the aligner know the exact distance between reads in a pair, so as to build a scaffold?
Or can only mate pairs do the latter? Are mate pairs still a thing? How does the aligner know the distance between two mates?
I realize these are quite basic questions, and apologize in advance.