I extracted some reads from a region (~200kb) of interest (including the unmapped ones) and all the pairs of unmapped reads from my WGS BAM: I'd like to know if it is possible to automatically (using vg?) detect any structural variant using the spades assembler (http://cab.spbu.ru/files/release3.12.0/manual.html ) for this region of interest .
Was just browsing and saw this question, maybe it is too late but oh well,
I wrote a tool called MUM&Co to compare de novo assemblies and I've tried it on many illumina assemblies and it seem to work well. Also there is Syri that does similar work. As they both explore the full range of SV types unlike Assemblytics.