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Bacterial ITS profiling updated 05/2020

16S rRNA gene-based microbial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a microbial profiling method based on the Internally Transcribed Spacer (ITS) region employing optimized primers and an ITS database for accurate cataloguing of bacterial communities at (sub)species resolution.


The Bacterial ITS profiling package is a complete tool for species-level profiling of complex bacterial communities based on the Internal Transcribed Spacer (ITS) region.


As prerequisites, the Bacterial ITS profiling package only requires Qiime2 to be installed in a linux environment.

A script for update of the ITS database (UMID) is also available for download.

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