Interviewee: Craig Venter.
Craig Venter talks about working with repeats.
The reason repeats are difficult for the mathematics of assembly, you can imagine if you only get six hundred letters of genetic code and if that matches exactly multiple spots in the genome, then you don't know where that piece goes. It's like working a jigsaw puzzle to have half the pieces all be identical to each other. That doesn't work very well. But if with that piece that's identical to many other spots in the genome, if at the other end of that piece of DNA you have a piece with a unique sequence on it, that allows you to anchor that unique sequence and in fact place that repeat, you'd then know where it goes.