A dual genome-methylome map of clonal evolution in grapevine — Analysis code

Custom analysis code and bioinformatics pipelines developed for the study "A dual genome-methylome map of clonal evolution in grapevine" (Callipo et al. 2026). The repository contains scripts for: diploid genome structural characterisation and annotation; diploid-aware somatic SNP and structural variant calling across 23 Pinot noir clones; methylation polymorphism (MP) identification using a binned binarisation approach; gene body methylation (GBM) classification; clonal lineage reconstruction; and validation of the ONT methylome against PacBio HiFi data. Full documentation is available at https://github.com/HGU-Plant-Breeding/23_Pinot_Clones.