Authors and affiliations
Petra Polakovicova1
1 Institute for Clinical and Experimental Medicine, Center for Experimental Medicine, Prague
General information
In this project, we evaluated 112 different bioinformatics pipeline configurations for processing 16S rRNA (V3-V4) amplicon sequencing data. Using the public available data of ZymoBIOMICS Microbial Community DNA as a reference standard, we assessed the accuracy and consistency of taxonomic profiles generated by each pipeline. Our results highlight the substantial variability introduced by different analysis strategies and emphasize the importance of developing validated and reproducible pipelines for microbiome data processing.
Methods
We used publicly available dataset (SRA accession number PRJNA674596) containing three technical replicates of the ZymoBIOMICS Microbial Community DNA standard (mock community). Then, we processed these reads by 112 bioinformatics pipeline configurations to compare the different results and analyze which factors change the result the most.
List of the pipeline configurations is available here. Final report can be found here.
Results
- Only 19% of pipelines accurately identified all taxa (F1 score = 1.0) while maintaining acceptable relative abundance (Bray-Curtis dissimilarity < 0.05).
- The most visible factor which changed the results is the usage of various denoising tools.
Content
analysis/data/contains merged ASV table, taxa table and metadata for this comparative analysisanalysis/scriptscontains source code of the analysis
This work was supported by MH CR – conceptual development of research organization (“Institute for Clinical and Experimental medicine - IKEM, IN 00023001”) and COST Action CA23110 “International networking on in vitro colon models simulating gut microbiota mediated interactions (INFOGUT).