:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-shortread' .. highlight: bash bioconductor-shortread ====================== .. conda:recipe:: bioconductor-shortread :replaces_section_title: :noindex: FASTQ input and manipulation :homepage: https://bioconductor.org/packages/3.18/bioc/html/ShortRead.html :license: Artistic-2.0 :recipe: /`bioconductor-shortread `_/`meta.yaml `_ :links: biotools: :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. .. conda:package:: bioconductor-shortread |downloads_bioconductor-shortread| |docker_bioconductor-shortread| :versions: .. raw:: html
1.60.0-01.58.0-01.56.0-11.56.0-01.52.0-21.52.0-11.52.0-01.50.0-01.48.0-1 ``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`` .. raw:: html
: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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 ``myenvname`` being 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: (see `bioconductor-shortread/tags`_ for valid values for ````) .. |downloads_bioconductor-shortread| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-shortread.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-shortread :alt: (downloads) .. |docker_bioconductor-shortread| image:: https://quay.io/repository/biocontainers/bioconductor-shortread/status :target: https://quay.io/repository/biocontainers/bioconductor-shortread .. _`bioconductor-shortread/tags`: https://quay.io/repository/biocontainers/bioconductor-shortread?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-shortread/README.html