- recipe bioconductor-dada2
Accurate, high-resolution sample inference from amplicon sequencing data
- Homepage:
- License:
LGPL-2
- Recipe:
- 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:
1.26.0-0
,1.22.0-2
,1.22.0-1
,1.22.0-0
,1.20.0-0
,1.18.0-1
,1.18.0-0
,1.16.0-0
,1.14.0-0
,1.26.0-0
,1.22.0-2
,1.22.0-1
,1.22.0-0
,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
>=0.44.0,<0.45.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-shortread
>=1.56.0,<1.57.0
bioconductor-xvector
>=0.38.0,<0.39.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
libstdcxx-ng
>=12
r-base
>=4.2,<4.3.0a0
r-ggplot2
>=2.1.0
r-rcpp
>=0.12.0
r-rcppparallel
>=4.3.0
r-reshape2
>=1.4.1
- Required By:
Installation
With an activated Bioconda channel (see 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-dada2/README.html)