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

Versions

1.42.0-1, 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 >=2.44.0,<2.45.0

• bioconductor-biocgenerics >=0.30.0,<0.31.0

• bioconductor-biocparallel >=1.18.0,<1.19.0

• bioconductor-biostrings >=2.52.0,<2.53.0

• bioconductor-genomeinfodb >=1.20.0,<1.21.0

• bioconductor-genomicalignments >=1.20.0,<1.21.0

• bioconductor-genomicranges >=1.36.0,<1.37.0

• bioconductor-iranges >=2.18.0,<2.19.0

• bioconductor-rsamtools >=2.0.0,<2.1.0

• bioconductor-s4vectors >=0.22.0,<0.23.0

• bioconductor-xvector >=0.24.0,<0.25.0

• bioconductor-zlibbioc >=1.30.0,<1.31.0

• libgcc-ng >=7.3.0

• libstdcxx-ng >=7.3.0

• r-base >=3.6,<3.7.0a0

• r-hwriter

• r-lattice

• r-latticeextra

Required By

• bioconductor-macpet

• bioconductor-girafe

• bioconductor-otubase

• bioconductor-quasr

• bioconductor-amplican

• bioconductor-htseqgenie

• bioconductor-scruff

• bioconductor-dada2

• bioconductor-rsffreader

• r-nanopore

• bioconductor-easyrnaseq

• bioconductor-arrayexpresshts

• bioconductor-ngsreports

• bioconductor-segmentseq

• bioconductor-systempiper

• bioconductor-edaseq

• bioconductor-basecallqc

• bioconductor-beat

• bioconductor-nucler

• bioconductor-esatac

• bioconductor-chipsim

• bioconductor-chipseqr

• bioconductor-r453plus1toolbox

• bioconductor-chipseq

• bioconductor-eatonetalchipseq

• bioconductor-rsvsim

• r-ngsplot

• bioconductor-gothic

• bioconductor-nestlink

• bioconductor-fastqcleaner

• bioconductor-rqc

• bioconductor-icetea

• bioconductor-ioniser

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>)

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-shortread/README.html)