scripts_and_plots

Collection of scripts to perform small bioinformatic analyses and generate plots.

1. Synteny plots for the study 'Genomic characterization of a nematode tolerance locus in sugar beet' (https://doi.org/10.1101/2023.06.22.546034).

   gggenomes_QTL_plot_overview.R

   gggenomes_QTL_plot_species.R

   Positions have to be added manually.

   The alignment was performed with minimap2: minimap2 -X -c file.fasta file.fasta > alignment_chr5.paf

   The scripts are based on the package 'gggenomes' (https://github.com/thackl/gggenomes).

   Both plots were combined into one figure (Figure 3 in the publication) using inkscape.