An introductory vignette demonstrating how to use the decontam package to identify contaminants.
The preprint introducing decontam with benchmarking demonstrating how
decontam-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive assocations.
More documentation available through the R help interface (e.g.
?isContaminant) and at the decontam web site.
The decontam R package is currently available as a source package through github, so installation requires the ability to compile R packages. This means that R and the R tool-chain must be installed, which requires the Xcode comnand-line tools on Mac and Rtools on Windows.
The easiest installation method uses the
Alternatively you can install from source by hand. First download the zipped package and unzip it (or expand the tarball). Start a fresh R session, and enter the following.
install.packages("path/to/dada2", repos = NULL, type = "source", dependencies = c("Depends", "Suggests","Imports"))
Bugs and difficulties in using decontam are welcome on the issue tracker.
Planned feature improvements are also publicly catalogued at on the "Issues" page for decontam: https://github.com/benjjneb/decontam/issues