Kmergenie fails to fit models with --diploid settings

Question

[pepijn.kooij]

I’ve been trying to run kmergenie on a trimmed dataset of MiSeq 2x300 paired end reads (trimmed with trimmomatic), using a list with the forward and reverse, paired and unpaired output from trimmomatic. When I run kmergenie with the normal haploid settings it works fine, but running it with --diploid many of the many of the kmer models are not able to fit the on the histograms (see screenshot of terminal+html files). Any idea why this is?

results without --diploid

results with --diploid

I really would like to be able to fit the diploid models, which I think would improve the kmer estimations, based on the fact that you can clearly see two humps in the histograms.

Hope you can help me out with this.

Answer 1

[Rayan Chikhi]

for the record: Pepijn and I communicated by email, and the diploid model has been improved in recent kmergenie versions, hopefully addressing this issue.