jamonterotena / Haplotype-based-Pangenome-Wheat-Analysis

This repository contains the files from my master thesis project required to conduct a whole-genome analysis of haploblocks in wheat based on pairwise comparisons between assemblies. This is based on a previous method (https://doi.org/10.1038/s42003-020-01413-2), but focuses on the the quality of the pairwise comparisons to call haplotypes.

- 'functions_hbpa.r' is required by every script in this repository

- 'template_hbpa.r' can be used to personalize parameters and source the script. All the information will come up on the console and in plots

- 'demonstration_rdma_hbpa.r' uses parameters from the haploblock RDMa, subject topic for the author's master thesis and can serve as an example of use

- 'Haplotype-based Pangenome Analysis in Wheat.pdf' presents an overview from the last script's outcome

- 'table_assembly_chr_length.txt' contains the chromosome length for all chromosomes in the 15 wheat assemblies

- 'alignment_props_supplementary_hbpa.r' was used for the master thesis to generate data on alignment properties from all rds files obtained by Brinton and colleagues and to apply a statistical analysis to prove the effects of using scaffolds as query in pairwise comparisons