:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bracken' .. highlight: bash bracken ======= .. conda:recipe:: bracken :replaces_section_title: :noindex: Bracken \(Bayesian Reestimation of Abundance with KrakEN\) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. :homepage: https://github.com/jenniferlu717/Bracken :license: GPL-3.0 :recipe: /`bracken `_/`meta.yaml `_ :links: biotools: :biotools:`Bracken`, doi: :doi:`10.7717/peerj-cs.104` .. conda:package:: bracken |downloads_bracken| |docker_bracken| :versions: .. raw:: html
2.9-02.8-12.8-02.7-02.6.2-02.6.1-32.6.1-22.6.1-12.6.1-0 ``2.9-0``,  ``2.8-1``,  ``2.8-0``,  ``2.7-0``,  ``2.6.2-0``,  ``2.6.1-3``,  ``2.6.1-2``,  ``2.6.1-1``,  ``2.6.1-0``,  ``2.6.0-2``,  ``2.6.0-1``,  ``2.6.0-0``,  ``2.5.3-0``,  ``2.5.2-0``,  ``2.5-2``,  ``2.5-1``,  ``2.5-0``,  ``2.2-1``,  ``2.2-0``,  ``1.0.0-1``,  ``1.0.0-0`` .. raw:: html
:depends _openmp_mutex: ``>=4.5`` :depends kraken2: :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :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 bracken and update with:: mamba update bracken To create a new environment, run:: mamba create --name myenvname bracken 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/bracken: (see `bracken/tags`_ for valid values for ````) .. |downloads_bracken| image:: https://img.shields.io/conda/dn/bioconda/bracken.svg?style=flat :target: https://anaconda.org/bioconda/bracken :alt: (downloads) .. |docker_bracken| image:: https://quay.io/repository/biocontainers/bracken/status :target: https://quay.io/repository/biocontainers/bracken .. _`bracken/tags`: https://quay.io/repository/biocontainers/bracken?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/bracken/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bracken/README.html