# Decontamination benchmarking The code provided here benchmarks six bioinformatic decontamination algorithms for microbiome sequencing data. This work is published as "Benchmarking MicrobIEM – a user-friendly tool for decontamination of microbiome sequencing data" in BMC Biology (details follow). The tested algorithms include the established frequency filter, Decontam frequency filter, Decontam prevalence filter, SourceTracker, presence filter, and the novel ratio and span filter implemented in our tool MicrobIEM (https://github.com/LuiseRauer/MicrobIEM). ## Even and staggered mock datasets R code files can be executed in any order. Files starting with "BM_" contain the functions for running the respective decontamination algorithms. Benchmarking of the decontamination algorithms for each dataset can be found in scripts starting with "1-3". The R code for analysing the mock communities can also be found at https://github.com/LuiseRauer/Decontamination_benchmarking. ## Skin microbiome dataset The R code files should be executed according to their starting number (0-6).