Additional file 1 of Systematic evaluation of B-cell clonal family inference approaches

Abstract

Additional file 1: Supplementary Figure 1. Data simulation pipeline. Simulation approach is an integration of ImmuneSim, Alakazam and SHazaM tools and equally use the data of CF groupings obtained from each of the 10 CF inference approaches. Supplementary Figure 2. Determination of the number of TP, TN, FP, and FN. Three simulated CFs (2 singletons) and two inferred CFs are shown. Supplementary Figure 3. Overall correlation between the log10(number of CFs) and the standardized sequence depth for all combinations of approach (except SCOPer; A7, A8) and dataset. Supplementary Figure 4. Overall trend between the log10(number of CFs) and the standardized mutation load for all combinations of approach (except SCOPer; A7, A8) and dataset. Supplementary Figure 5. Summary of significant pairwise comparisons between Approaches. Supplementary Figure 6. Number of TP, TN, FP, and FN cases produced by the ten approaches when applied to six samples from three simulated datasets (D10, D11, D12). Supplementary Figure 7. Normalized number of TP, TN, FP, and FN cases produced by the ten approaches when applied to six samples from three simulated datasets (D10, D11, D12)