:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-rfastp' .. highlight: bash bioconductor-rfastp =================== .. conda:recipe:: bioconductor-rfastp :replaces_section_title: :noindex: An Ultra\-Fast and All\-in\-One Fastq Preprocessor \(Quality Control\, Adapter\, low quality and polyX trimming\) and UMI Sequence Parsing\). :homepage: https://bioconductor.org/packages/3.18/bioc/html/Rfastp.html :license: GPL-3 + file LICENSE :recipe: /`bioconductor-rfastp `_/`meta.yaml `_ Rfastp is an R wrapper of fastp developed in c\+\+. fastp performs quality control for fastq files. including low quality bases trimming\, polyX trimming\, adapter auto\-detection and trimming\, paired\-end reads merging\, UMI sequence\/id handling. Rfastp can concatenate multiple files into one file \(like shell command cat\) and accept multiple files as input. .. conda:package:: bioconductor-rfastp |downloads_bioconductor-rfastp| |docker_bioconductor-rfastp| :versions: .. raw:: html
1.12.0-01.10.0-01.8.0-11.8.0-01.4.0-21.4.0-11.4.0-01.2.0-01.0.0-2 ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-1``,  ``1.8.0-0``,  ``1.4.0-2``,  ``1.4.0-1``,  ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-2``,  ``1.0.0-1`` .. raw:: html
:depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0`` :depends bioconductor-rhtslib: ``>=2.4.0,<2.5.0a0`` :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-ggplot2: :depends r-rcpp: :depends r-reshape2: :depends r-rjson: :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-rfastp and update with:: mamba update bioconductor-rfastp To create a new environment, run:: mamba create --name myenvname bioconductor-rfastp 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-rfastp: (see `bioconductor-rfastp/tags`_ for valid values for ````) .. |downloads_bioconductor-rfastp| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-rfastp.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-rfastp :alt: (downloads) .. |docker_bioconductor-rfastp| image:: https://quay.io/repository/biocontainers/bioconductor-rfastp/status :target: https://quay.io/repository/biocontainers/bioconductor-rfastp .. _`bioconductor-rfastp/tags`: https://quay.io/repository/biocontainers/bioconductor-rfastp?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-rfastp/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-rfastp/README.html