recipe bioconductor-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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/dada2.html

License

LGPL-3

Recipe

/bioconductor-dada2/meta.yaml

Links

biotools: dada2

package bioconductor-dada2

(downloads) docker_bioconductor-dada2

Versions

1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.4-0, 1.4.0-0, 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

>=0.28.0,<0.29.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-shortread

>=1.40.0,<1.41.0

Depends bioconductor-xvector

>=0.22.0,<0.23.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

>=1.9.4

Depends r-ggplot2

>=2.1.0

Depends r-rcpp

>=0.11.2

Depends r-rcppparallel

>=4.3.0

Depends r-reshape2

>=1.4.1

Requirements

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>)