Paired end sequencing reffers to sequrncing of fragments from both ends ...this is in contrast to single end sequemcing where sequencing is done from one end only.
Because the distance between each paired read is known, alighnment algorithms can use this information to map the reads over
Repititive regions more precisely.
This results in much better alighnment of reads, especially across difficult to sequence, repetituve regions of the genome.
