Fig. 4

Impact of various parameters on the performance of Kraken. Schematic representation of the sets of factor combinations for investigating their impact on the performance of the Kraken tool, which was used in the three best-performing pipelines. Combinations shaded in grey were not investigated (A). The impact of quality control read filtering (B), database version (C), database completeness (D), and count estimate by using Bracken (E) were evaluated. The absolute difference in F1 scores or weighted UniFrac scores between two options (option 1 on the left and option 2 on the right side for each diverging bar chart) were calculated for each dataset for the factors investigated. The color of the bars illustrates whether the option 1 (blue) or option 2 (red) had a larger score