k-mer GWAS for the wheat leaf rust pathogen

This repository contains codes used in Tsushima et al., 2025, bioRxiv.

Fig.1 Genetic diversity among Pt, Pgt and Pst.

Fig.2 Phylogenetic analysis of Pt isolates.

Fig.3 k-mer-based GWAS using HAWK (Rahman et al., 2018, eLife).

Fig.4 Manhattan plots.

Fig.5 Transcriptome analyses using lab and field RNA-seq data.

Fig.6 Genome alignments and mapping analysis to identify structural variations.