https://github.com/benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
https://github.com/benjjneb/decontam
amplicon bioinformatics contamination metabarcoding metagenomics microbiome
Last synced: 3 months ago
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Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
- Host: GitHub
- URL: https://github.com/benjjneb/decontam
- Owner: benjjneb
- Created: 2017-04-04T03:20:13.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2025-09-04T21:35:55.000Z (9 months ago)
- Last Synced: 2025-10-20T14:46:17.138Z (7 months ago)
- Topics: amplicon, bioinformatics, contamination, metabarcoding, metagenomics, microbiome
- Language: HTML
- Homepage: https://benjjneb.github.io/decontam/
- Size: 1.25 MB
- Stars: 163
- Watchers: 10
- Forks: 26
- Open Issues: 97
-
Metadata Files:
- Readme: README.md
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README
## Documentation
**An [introductory vignette](https://benjjneb.github.io/decontam/vignettes/decontam_intro.html) demonstrating how to use the decontam package to identify contaminants.**
**An [extensive investigation of contamination](https://benjjneb.github.io/DecontamManuscript/Analyses/oral_contamination.html) in an oral mucosal dataset, that includes evaluation of deontam results.**
**The [manuscript introducing decontam](https://doi.org/10.1186/s40168-018-0605-2) with benchmarking demonstrating how `decontam`-inating your data removes reagent sequences, improves accuracy, reduces batch effects, and prevents false-positive associations.**
More documentation available through the R help interface (e.g. `?isContaminant`) and at [the decontam web site](https://benjjneb.github.io/decontam).
## Installation
The decontam R package is most easily installed from the Bioconductor repository. To install the most recent version of the decontam package, start R (version "3.6") and enter:
```S
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("decontam")
```
See [the Bioconductor documentation for decontam](https://bioconductor.org/packages/release/bioc/html/decontam.html) for additional information.
The decontam R package is also available as a source package through github. 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](http://railsapps.github.io/xcode-command-line-tools.html) on Mac and [Rtools](https://cran.r-project.org/bin/windows/Rtools/) on Windows.
The easiest source installation method uses the `devtools` package:
```S
library(devtools)
devtools::install_github("benjjneb/decontam")
```
## Other Resources
Bugs and difficulties in using decontam are welcome on [the issue tracker](https://github.com/benjjneb/decontam/issues).
Planned feature improvements are also publicly catalogued at on the "Issues" page for decontam: https://github.com/benjjneb/decontam/issues