Supplementary data: Comparison of target enrichment strategies for ancient pathogen DNA

Supplementary Note 1 – Laboratory workflow Supplementary Note 2 - Bioinformatics and Statistical Analysis Supplementary Note 3 – Results of the Bioinformatics and Statistical Analysis Supplementary Figure 1: Comparison of (A) mean coverage, (B) standard deviation of the mean coverage, (C) enrichment factor, (D) and the percentage of the genome covered 5 fold, (E) distribution of the fragment length and (F) frequency of the aDNA damage for the ancient and modern strains of M. leprae. Three independent replicates were performed for each method. Labels of the ancient samples are in black and for the modern samples in red. Boxplots of the array are blue, of the DNA bait capture red and the RNA baits capture is green and grey for the first and second round, respectively Supplementary Figure 2: Comparison of (A) mean coverage, (B) standard deviation of the mean coverage, (C) enrichment factor, (D) and the percentage of the genome covered 5 fold, (E) distribution of the fragment length and (F) frequency of the aDNA damage for the ancient and modern strains of T. pallidum. Three independent replicates were performed for each method. Labels of the ancient samples are in black and for the modern samples in red. Boxplots of the array are blue, of the DNA bait capture red and the RNA baits capture is green and grey for the first and second round, respectively Supplementary Figure 3: Number of unique reads for the three replicate batches of the three tested methods. The number of unique reads in the second round of hybridization with the RNA baits does not strongly increase compared to the first round. Supplementary Table 1: List of all samples used in this study group according to organism and age together with the original publications. Supplementary Table 4: Comparison of the specific reads of the three tested protocols. Supplementary Table 6: Comparison of the variance within each method tested. Supplementary Table 7: Comparison of the costs per reaction.