DIPLER: rapid k-mer-based locus identification

Authors

Kivirüüt, K. R., Kaplinski, L., Salumets, A., Puurand, T.

Abstract

Here, we present Dipler, a two-step strategy that combines the identification of group-specific k-mers from whole-genome sequencing data with de novo assembly of PacBio reads enriched for those k-mers. Using a Gg/gg presence/absence-like model in Juglans hindsii, we recovered the structurally distinct "G" allele from PacBio reads at coverage as low as 9x. Using the exceptional GG genotype of J. regia "Sharkey" as a complementary diploid model, we further show that two divergent "G" alleles of the same locus can be resolved and assembled separately from 13x coverage. Dipler therefore provides a rapid, reference-independent framework for identifying structurally complex loci, with potential applicability across eukaryotic species.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Oct 2026.

Stats

1-terrible, 9-excellent. How would you rate this preprint? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.