malonge
correct use by the species.
I would like to correct the genome of Inia geoffrensis, but the closest genome I have available for correction is from Lipotes vexillifer. These two species belong to different genera and have been separated by several million years of evolution. I'm uncertain about the extent to which the correction will be effective since they are different species.
Hi!
I am using ragtag correct for a similar purpose — my reference organism diverged a few Mya from my drafts. In my case it seems to produce sensible results when I input draft reads for validation along with the assembly — although it's plants, not animals, and still considered as one genus. Still, there are always a few misassemblies which are corrected and a few real translocations which are kept.
I would say that generally it depends on the rate of genome evolution in your system. Maybe ragtag correct would struggle or make mistakes if recombination rate was too big, but I think you could give it a try and keep a little scepticism about the output.
