:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bowtie2' .. highlight: bash bowtie2 ======= .. conda:recipe:: bowtie2 :replaces_section_title: :noindex: Fast and sensitive gapped read alignment :homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml :license: GPL3 / GPL-3.0-only :recipe: /`bowtie2 `_/`meta.yaml `_ :links: biotools: :biotools:`bowtie2`, doi: :doi:`10.1038/nmeth.1923`, debian: :debian:`bowtie2`, usegalaxy-eu: :usegalaxy-eu:`bowtie2` .. conda:package:: bowtie2 |downloads_bowtie2| |docker_bowtie2| :versions: .. raw:: html
2.5.3-12.5.3-02.5.2-02.5.1-22.5.1-12.5.1-02.5.0-02.4.5-42.4.5-3 ``2.5.3-1``,  ``2.5.3-0``,  ``2.5.2-0``,  ``2.5.1-2``,  ``2.5.1-1``,  ``2.5.1-0``,  ``2.5.0-0``,  ``2.4.5-4``,  ``2.4.5-3``,  ``2.4.5-2``,  ``2.4.5-1``,  ``2.4.5-0``,  ``2.4.4-1``,  ``2.4.4-0``,  ``2.4.3-0``,  ``2.4.2-2``,  ``2.4.2-1``,  ``2.4.2-0``,  ``2.4.1-3``,  ``2.4.1-2``,  ``2.4.1-1``,  ``2.4.1-0``,  ``2.3.5.1-0``,  ``2.3.5-0``,  ``2.3.4.3-1``,  ``2.3.4.3-0``,  ``2.3.4.2-0``,  ``2.3.4.1-1``,  ``2.3.4.1-0``,  ``2.3.4-0``,  ``2.3.3.1-0``,  ``2.3.2-1``,  ``2.3.0-1``,  ``2.3.0-0``,  ``2.2.8-2``,  ``2.2.8-1``,  ``2.2.8-0``,  ``2.2.7-1``,  ``2.2.7-0``,  ``2.2.6-0``,  ``2.2.5-8``,  ``2.2.5-7``,  ``2.2.5-6``,  ``2.2.5-5``,  ``2.2.5-4``,  ``2.2.5-3``,  ``2.2.5-2``,  ``2.2.5-1``,  ``2.2.4-8``,  ``2.2.4-7``,  ``2.2.4-6``,  ``2.2.4-5``,  ``2.2.4-4``,  ``2.2.4-3``,  ``2.2.4-2``,  ``2.2.4-1``,  ``2.2.4-0``,  ``2.2.1-5``,  ``2.2.1-4``,  ``2.2.1-3``,  ``2.2.1-2``,  ``2.2.1-1``,  ``2.2.1-0`` .. raw:: html
:depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends perl: :depends python: ``>=3.10,<3.11.0a0`` :depends python_abi: ``3.10.* *_cp310`` :depends tbb: ``>=2021.11.0`` :depends zlib: :depends zstd: ``>=1.5.5,<1.6.0a0`` :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 bowtie2 and update with:: mamba update bowtie2 To create a new environment, run:: mamba create --name myenvname bowtie2 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/bowtie2: (see `bowtie2/tags`_ for valid values for ````) .. |downloads_bowtie2| image:: https://img.shields.io/conda/dn/bioconda/bowtie2.svg?style=flat :target: https://anaconda.org/bioconda/bowtie2 :alt: (downloads) .. |docker_bowtie2| image:: https://quay.io/repository/biocontainers/bowtie2/status :target: https://quay.io/repository/biocontainers/bowtie2 .. _`bowtie2/tags`: https://quay.io/repository/biocontainers/bowtie2?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/bowtie2/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bowtie2/README.html