astrobiomike / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

Documentation

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.

Peer-reviewed publication can be found here.

More documentation available through the R help interface (e.g. ?isContaminant) and at the decontam web site.

Installation

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 command-line tools on Mac and Rtools on Windows.

The easiest installation method uses the devtools package:

library(devtools)
devtools::install_github("benjjneb/decontam")

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/decontam", repos = NULL, type = "source",
                 dependencies = c("Depends", "Suggests","Imports"))

Other Resources

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