Advantages of paired-end sequencing compared to single end One of the advantages of paired end sequencing over single end is that it doubles the amount of data. Another supposed advantage is that it leads to more accurate reads because if say Read 1 (see picture below) maps to two different regions of the genome, Read 2 can be used to help determine which one of the two regions makes more sense. However, I don't understand how this second advantage pertains only to paired end sequencing. With single-end sequencing, couldn't you just use the read that comes right after read 1 to essentially get a longer net read?
In paired-end sequencing, you have an expected fragment length. So if Read 1 maps to two different places, whereas Read 2 only maps to one place. Then you can determine which one is more likely for Read 1 to map to. It cannot be too far away from Read 2 given the expected fragment length.
It is not necessarily true that paired-end sequencing gets twice the amount of data. The total amount of data can be determined when running sequencing. If single-end has 20M reads, I can just stop sequencing at 20M as well for paired-end.