:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cutadapt' .. highlight: bash cutadapt ======== .. conda:recipe:: cutadapt :replaces_section_title: :noindex: Trim adapters from high\-throughput sequencing reads :homepage: https://cutadapt.readthedocs.io/ :developer docs: https://github.com/marcelm/cutadapt :license: MIT / MIT :recipe: /`cutadapt `_/`meta.yaml `_ :links: biotools: :biotools:`cutadapt`, doi: :doi:`10.14806/ej.17.1.200`, usegalaxy-eu: :usegalaxy-eu:`cutadapt` .. conda:package:: cutadapt |downloads_cutadapt| |docker_cutadapt| :versions: .. raw:: html
4.7-14.7-04.6-24.6-14.6-04.5-04.4-14.4-04.3-0 ``4.7-1``,  ``4.7-0``,  ``4.6-2``,  ``4.6-1``,  ``4.6-0``,  ``4.5-0``,  ``4.4-1``,  ``4.4-0``,  ``4.3-0``,  ``4.2-0``,  ``4.1-1``,  ``4.1-0``,  ``4.0-0``,  ``3.7-1``,  ``3.7-0``,  ``3.6-0``,  ``3.5-1``,  ``3.5-0``,  ``3.4-1``,  ``3.4-0``,  ``3.3-1``,  ``3.3-0``,  ``3.2-0``,  ``3.1-0``,  ``3.0-0``,  ``2.10-1``,  ``2.10-0``,  ``2.9-0``,  ``2.8-0``,  ``2.7-0``,  ``2.6-0``,  ``2.5-0``,  ``2.4-0``,  ``2.3-0``,  ``2.2-0``,  ``2.1-0``,  ``2.0-0``,  ``1.18-1``,  ``1.18-0``,  ``1.17-0``,  ``1.16-2``,  ``1.16-1``,  ``1.16-0``,  ``1.15-0``,  ``1.14-0``,  ``1.13-0``,  ``1.12-1``,  ``1.12-0``,  ``1.11-0``,  ``1.10-0``,  ``1.9.1-0``,  ``1.8.3-0``,  ``1.8.1-0`` .. raw:: html
:depends dnaio: ``>=1.2.0`` :depends libgcc-ng: ``>=12`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends xopen: ``>=1.6.0`` :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 cutadapt and update with:: mamba update cutadapt To create a new environment, run:: mamba create --name myenvname cutadapt 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/cutadapt: (see `cutadapt/tags`_ for valid values for ````) .. |downloads_cutadapt| image:: https://img.shields.io/conda/dn/bioconda/cutadapt.svg?style=flat :target: https://anaconda.org/bioconda/cutadapt :alt: (downloads) .. |docker_cutadapt| image:: https://quay.io/repository/biocontainers/cutadapt/status :target: https://quay.io/repository/biocontainers/cutadapt .. _`cutadapt/tags`: https://quay.io/repository/biocontainers/cutadapt?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/cutadapt/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cutadapt/README.html