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Code and scripts for Ae. tauschii diversity analysis

License: GNU General Public License v3.0

R 90.28% Shell 9.72%

code_ae_tauschiidiversity's Introduction

Repository for scripts and other data analysis protocols for Aegilops tauschii diversity project.

  1. Run Tassel5 GBSv2 pipeline using the provided keyfile in SNP_calling_scripts folder to call SNPs.

  2. required_files contain files with some required metadata.

  3. Use the R scripts to perform a specific analysis.

    • 1.File.formatting.R - format hapfile for further analyses
    • 2.SNP.Filtering.R - filter SNPs based on criteria given in the paper
    • 3.PCA_Cluster.R - plot PCA plots, biplots, and violin plots
    • 4.Genetic.diversity.R - compute genetic diversity statistics
    • 5_Hybrid_graphical.R - plot hybrids graphically

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