whealbiCode

Custom source code, workflows and jupyter notebooks used in the analysis of the wheat genotypes sequenced in the Whealbi Project

Analysis Workflow

1. Raw Data Processing and Variant Calling
2. Genome-Wide Association Study (Figure 1)
3. Geographical component of the panel structure (Figure 2A)
4. Components of the panel structure (Figure 2B)
5. Computation of nucleotide diversity π (Figure 3)
6. Studying the Phylogeny and Reticulate Evolution of the Wheat Species Complex using Repeated Random Haplotype Sampling (RRHS; Figure 4)
7. Inference of Hybridization and Introgression Events using ABBA-BABA (Figure 4B)