Fig. 2
From: Benchmarking MicrobIEM – a user-friendly tool for decontamination of microbiome sequencing data
Sample composition and level of contamination by dilution in the mock communities used for benchmarking. The proportion of contaminants increases with decreasing amount of bacterial input material, both in the even mock community (A) and in the two staggered mock communities A and B (B, C). The even mock community (A) contains species of 6–22% expected relative abundance, and comprises threefold serial dilutions from 1.5 × 109 to 2.3 × 105 bacterial input cells and one pipeline negative control (NEG). The staggered mock community A (B) contains species of 0.18–18% expected relative abundance, and comprises tenfold serial dilutions from 1 × 109 to 1 × 102 bacterial input cells and three pipeline negative controls (NEG). The staggered mock community B (C) contains species of 3–84.3% expected relative abundance, and comprises 20-fold serial dilutions from 1.1 × 105 to 5.55 × 103 bacterial input cells and four pipeline negative controls (NEG). Each bar in B shows the mean composition per triplicate (103: duplicate) per dilution, and each bar in C shows the mean composition over four replicates per dilution. Reads not matching expected sequences were defined as contaminants (see details in “Methods”). Dilutions highlighted in bold are selected for decontamination benchmarking