DIPLER: rapid k-mer-based locus identification

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.