Hi,
I am trying to use a pangenome approach to compare 5 Fusarium proliferatum isolates that have been assembled using Nanopore/Illumina reads. However, one of the isolates has a major translocation and inversion (~1.8Mb) between the 5' end of chr1 and the 3' end of chr3, and I'm not sure the best way forward with this. I have used a pangenome graph approach with Minigraph Cactus for some other preliminary analyses, but from my understanding, Minigraph Cactus may not be able to deal with the large translocation/inversion. I have already tried using Ragtag correct with and without read verification to break this translocation and then scaffold back with Ragtag scaffold, but it is resistant to this.
Does anyone have any advice that they can throw my way?
It isn't clear exactly what you want to do but you could try PGGB instead. This has no problem with alignments between translocated regions.
However, I am surprised that minigraph-cactus would have an issue. As it is fast-ish to run; you could just try it and see?