recipe bioconductor-shortread

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Homepage

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

License

Artistic-2.0

Recipe

/bioconductor-shortread/meta.yaml

Links

biotools: shortread

package bioconductor-shortread

(downloads) docker_bioconductor-shortread

Versions

1.40.0-0, 1.38.0-0, 1.36.0-0, 1.34.2-0, 1.32.0-0, 1.28.0-0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicalignments

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-xvector

>=0.22.0,<0.23.0

Depends bioconductor-zlibbioc

>=1.28.0,<1.29.0

Depends libgcc-ng

>=7.3.0

Depends libstdcxx-ng

>=7.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-hwriter

Depends r-lattice

Depends r-latticeextra

Requirements

Installation

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

conda install bioconductor-shortread

and update with:

conda update bioconductor-shortread

or use the docker container:

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

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