Need to evaluate two large (1Gb) chromosome-level assemblies of the same genome by means of finding large structural variations between the two (duplication, inversion, deletion etc). I am trying to use
minimap2 to get this sort of statistics (similiar to somewhat classical
show-diff approach), but I couldn't find any parser for .paf files (only
paftools.js from minimap' creator, but it does not produce desired statistics). Conversion of .paf to .delta and using dna-diff is somehow imperfect.
Do you know any parser of .paf files for finding stuctural variations? Or a workaroung of a problem comparing two large assemblies? Many thanks!