recipe bioconductor-dada2

Accurate, high-resolution sample inference from amplicon sequencing data

Homepage

https://bioconductor.org/packages/3.13/bioc/html/dada2.html

License

LGPL-2

Recipe

/bioconductor-dada2/meta.yaml

Links

biotools: dada2

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

package bioconductor-dada2

Versions

1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.10.0-0,  1.8.0-0,  1.6.0-0, 

1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.4-0,  1.2-0,  1.0.3-0,  0.99.10-0,  0.10.4-0,  0.10.3-0,  0.10.1-0,  0.10.0-0

Depends

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-shortread >=1.50.0,<1.51.0

• bioconductor-xvector >=0.32.0,<0.33.0

• libblas >=3.8.0,<4.0a0

• libgcc-ng >=9.3.0

• liblapack >=3.8.0,<4.0a0

• libstdcxx-ng >=9.3.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2 >=2.1.0

• r-rcpp >=0.12.0

• r-rcppparallel >=4.3.0

• r-reshape2 >=1.4.1

Required By

• lotus2

• dadaist2

• amptk

• bioconductor-rbec

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-dada2

and update with:

conda update bioconductor-dada2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-dada2:<tag>

(see bioconductor-dada2/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-dada2/README.html)