Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Supplementary data for the paper "Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing" tools_cmd - command lines and relevant scripts for running all tools benchmarking - CNA profiles and scripts used for benchmarking castle_normal_assmelies - De novo assmeblies of matching normal CASTLE cell lines (HC1954BL, HCC1937BL, BL2009, BL1437 and BL1395) cna_profiles_visualization_castle - Chromosome profiles visualization for all tools for the CASTLE cell lines castle_benchmarks - Outputs and benchmarking scores for all tools on the CASTLE datasets breast_cell_lines - Wakhan outputs for the breast cancer cell lines panel downsampled_HCC1954 - Outputs and benchmarking scores for all tools on the downsampled HCC1954 datasets downsampled_H1437 - Outputs and benchmarking scores for all tools on the downsampled H1437 datasets timing_scripts - Scripts used for the mutation timing analysis