- recipe bioconductor-shortread
FASTQ input and manipulation
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/ShortRead.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: 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.
- package bioconductor-shortread¶
- versions:
1.60.0-0,1.58.0-0,1.56.0-1,1.56.0-0,1.52.0-2,1.52.0-1,1.52.0-0,1.50.0-0,1.48.0-1,1.60.0-0,1.58.0-0,1.56.0-1,1.56.0-0,1.52.0-2,1.52.0-1,1.52.0-0,1.50.0-0,1.48.0-1,1.48.0-0,1.46.0-0,1.44.0-0,1.42.0-1,1.40.0-0,1.38.0-0,1.36.0-0,1.34.2-0,1.32.0-0,1.28.0-0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-xvector:
>=0.42.0,<0.43.0- depends bioconductor-xvector:
>=0.42.0,<0.43.0a0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-hwriter:
- depends r-lattice:
- depends r-latticeextra:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-shortread and update with:: mamba update bioconductor-shortread
To create a new environment, run:
mamba create --name myenvname bioconductor-shortread
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-shortread:<tag> (see `bioconductor-shortread/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-shortread/README.html)
