- local aggregation for subtracting hetmers containing sequencing errors
- fishnet algorithm for 1n coverage fit
Known problems:
- quantification of higher ploidy smudges is not well reflecting higher coverage variance and therefore leads to "overspilling" of kmers pairs to other smudges;
- Sometimes for species with strong tetraploid signal and weak diploid signal, the fit is better for assigning the 4n smudge as 2n. This is a recognisable pattern and clear limitation of the optimisation criteria we use at the moment. We are working on fixing this.
- We removed explicit ploidy predictions, users need to make a join interpretation of smudgeplot, genomescope and prior knowledge about to species to determine the most sensible ploidy. An explicit ploidy level is our preferred solution to both problems listed above, so hopefully this functionality will return.