We recently performed a study to understand the impact of decreasing microbial biomass on 16S rRNA gene sequencing experiments and evaluate the current computational strategies to control for contaminants (available here).
This repository contains the compiled R Markdown documents to reproduce the analysis presented in the manuscript, divided into 6 primary sections:
- Introduction and evaluating contaminants
- Removing contaminant ASVs with filtering methods
- Removing contaminant ASVs with decontam
- Removing contaminant ASVs with SourceTracker
- Evaluating SourceTracker results
- Final evaluation of all methods
We hope that this will serve as a resource and tutorial for those wishing to use these computational approaches on their own data.
We have a Binder so that the code in this repository can be run without having to install R/RStudio and all associated packages used. To access, click the Launch Binder logo below (it may take a bit to load).
