Additional file 1 of Benchmarking MicrobIEM – a user-friendly tool for decontamination of microbiome sequencing data

Additional file 1: TabS1. Overview of datasets for benchmarking of bioinformatic decontamination tools. TabS2. Overview of strain and growth information of bacterial taxa used for the staggered mock community A. TabS3. Overview of common contaminants based on a literature search. TabS4. Overview of publications used for classification of typical skin inhabitants. TabS5. Typical skin inhabitants with appearance in at least three out of seven publications. FigS1. Schematic overview of decontamination filters implemented in MicrobIEM. FigS2. Schematic overview of MicrobIEM workflow for quality control and microbiome analysis. FigS3. Benchmarking of MicrobIEM’s ratio and span filter in the staggered mock communities. FigS4. Additional evaluation measures in the decontamination benchmarking of mock communities. FigS5. Precision-recall curves for decontamination benchmarking of mock communities. FigS6. Effect of decontamination algorithms in the low-biomass skin microbiome dataset. FigS7. Effect of decontamination algorithms on the top 10 genera in the low-biomass skin microbiome dataset. FigS8. Reduction of reads and features in the low-biomass skin microbiome dataset by decontamination tools. FigS9. Screenshots of graphical support for additional quality control measures with MicrobIEM.