fanli-gcb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution

dada2

Exact sample inference from high-throughput amplicon data. Resolves real variants differing by as little as one nucleotide. Visit the DADA2 website for the most detailed and up-to-date documentation.

Installation

The dada2 package binaries are available through Bioconductor:

## try http:// if https:// URLs are not supported
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("dada2")

In order to install dada2 from source (and get the latest and greatest new features) see our installation from source instructions.

Documentation

The tutorial walkthrough of the DADA2 pipeline on paired end Illumina Miseq data.

The dada2 R package manual.

Further documentation is available on the DADA2 front page.

DADA2 Articles

DADA2: High resolution sample inference from Illumina amplicon data. Nature Methods, 2016. (Open Access link.)

Bioconductor workflow for microbiome data analysis: from raw reads to community analyses. F1000 Research, 2016.

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISMEJ, 2017.

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Research, 2019.

Other Resources

Planned feature improvements are publicly catalogued at the main DADA2 development site on github, specifically on the "Issues" page for DADA2:

https://github.com/benjjneb/dada2/issues

If the feature you are hoping for is not listed, you are welcome to add it as a feature request "issue" on this page. This request will be publicly available and listed on the page.

Bugs and difficulties in using DADA2 are also welcome on the issue tracker.