Given a de novo assembly and a reference assembly, what methods have you tried / would you recommend for determining structural variations?
For this paper [An integrated map of structural variation in 2,504 human genomes][1] my tiny part was to validate complex structural variation in long read TruSeq data.

It was about 3 years ago so I'm not sure if there are better approaches. But we created breakpoint contigs across putative SV breakpoints using Velvet.

Then I took the breakpoint contigs (there are many possible ones generated by Velvet) and I used BLAT to align them to the reference genome. 

Using the BLAT results I was able to parse out the precise breakpoints.

Like I said it's rather labor intensive and I'm sure there's a better way of doing it. But this might be a good lead!


  [1]: http://www.nature.com/nature/journal/v526/n7571/abs/nature15394.html