Fig. 1

Overview of the decontamination benchmarking study design. Three mock datasets were used for decontamination benchmarking, one with an even, and two with a staggered community structure. Mock communities were available as dilution series covering a wide range of bacterial biomass per sample (10⁸ to 5.55 × 10³ bacterial cells). Two sample-based and five control-based decontamination algorithms were compared based on their classification performance into mock and contaminant reads, evaluated by Youden’s index and other evaluation scores. The same parameters and tools were also evaluated in a low-biomass environmental dataset from the skin. Additional information about the decontamination filters implemented in MicrobIEM can be found in Additional file 1: Supplementary Figure 1