Hello everyone !
I'm looking for a way to asses the quality my long PacBio reads assembly. I already tried Quast, which gives you all the classical metrics for genome assembly assessment. I also tried Busco2, which give you a preview of the duplication level within a set of particular genes (exemple : arthropoda, insecta...), but I need something more specific.
I my long read assembly, as the studied species is higly polymorphic, I already spotted on particular gene local duplication within the assembly. For example, a gene, with the following exon structure : 1 2 3 4 in the closest species D.melanogaster, will be duplicated with a false exon structure : 1 3 4 2 3 4.
I've heard about amosvalidate pipeline, which identify "suspicious" regions. But I'm not sure that this pipeline is well suited for my data.
Do you have any idea of what tool or method I can use in order to detect this particular kind of events ?
Thanks for your advices !