I want to compare my assembled genome with a reference for structural variation. Most SV methods map resequenced paired-end reads to the reference such as SVdetect, BreakDancer etc. However, my main source of long range information are pacbio reads. I have also done a hybrid assembly. I have two questions:
1. Is there a principled way and established pipeline to use pacbio reads for structural variation detection? I know raw PB reads will be problematic because of their high error rates. One approach is to map raw reads to region of interest, do a local assembly and polishing. Is there an established pipeline for this.
2. A different approach would be to use assembled genomes. I can compare the genomes with MUMmer. Is there a standard software people use for taking the MUMmer output and getting a list of structural variations? Is there a way to gain confidence in terms of what is misassembly vs. structural variation? I know Sibelia uses whole genome alignment but it is advertised for microorganisms. Would it work for more complex genomes like plants?