Codes and supplementary materials for the coming manuscript on mutation accumulation in DNA repair deficient C. elegans.

B. Meier, N. Volkova, Y Hong, S Bertolini, B Wang, V Gonzalez-Huici, S Boulton, PJ Campbell, M Gerstung and A Gartner

"Protection of the C. elegans germ cell genome depends on diverse DNA repair pathways during normal proliferation"

The manuscript is currently under preparation. For any questions or suggestions, please contact me via [email protected].

Script structure:

Location_plots.Rmd - contains the plotting of mutation distributions across the genome in multiple samples and clustering analysis. Requires samples annotation table, lists of VCFs for base substitutions and indels, as well as a table of structural variants.

Mutation_rate_estimation_final.R - codes for estimation of mutation rates and mutational signatures, analysis of differences to wild-type, and figure plotting. Requires a matrix with mutation counts and sample annotation table.

SV_info.R - in-depth analysis of structural variants

dog_1_analysis.R - separate script producing plot with distributions of G4 and non-G4 associated mutations in dog-1 mutants.

plotting_complex_SVs.R - separate script for plotting complex structural variants, requires a table of SVs as well as .bw and bamstat files for each sample (including the reference samples).

plotting_functions.R - supplementary fuctions for signature plotting.

useful_functions.R - supplementary functions for analysis.