Fig. 2

Comparison of different library strategies for DNA mock communities. A Percentage of phage genomes with dsDNA T4 generated by different library preparation methods. Different colors indicate different phage genomes. B Principal coordinates analysis (PCoA) plots of bray–Curtis distance matrices. PCoA was used to plot the beta diversity of mock-associated communities using the bray matrix. Different colors indicate different library preparation methods, and different shapes indicate different DNA mock communities. The dark-filled shapes display the mock with dsDNA T4 genome and the non-filled without dsDNA T4. For each axis, in square brackets, the percentage of variation explained was reported. C Percentage of phage genomes without dsDNA T4 genome. D Pearson correlation coefficient (r) and two-tailed p-value between the expected and obtained read distributions (in percentage) in different DNAs phage mock communities with (top panel) or without (bottom panel) phage T4 genome. Five different libraries were used to prepare and sequence three artificial bacteriophage mocks containing different proportions of the ssDNA phage (phiX174 and M13mp18) mixed with the dsDNA phage. These phage genome abundance values were calculated based on the quantity of dsDNA and ssDNA phages measured Qubit dsDNA (or ssDNA) HS Assay kit. MA, Mock A with a ratio of ~ 90:10 for dsDNA and ssDNA; MB, Mock B with a ratio of ~ 50:50 for dsDNA and ssDNA; MC, Mock C with a ratio of ~ 10:90 for dsDNA and ssDNA