-
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
- Links
biotools: shortread
-
package
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>)
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-shortread/README.html)