:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'quast'
.. highlight: bash

quast
=====

.. conda:recipe:: quast
   :replaces_section_title:
   :noindex:

   Quality Assessment Tool for Genome Assemblies.

   :homepage: https://quast.sourceforge.net
   :documentation: https://quast.sourceforge.net/docs/manual.html
   
   :developer docs: https://github.com/ablab/quast
   :license: Custom
   :recipe: /`quast <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/quast>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/quast/meta.yaml>`_
   :links: biotools: :biotools:`quast`, usegalaxy-eu: :usegalaxy-eu:`quast`, doi: :doi:`10.1093/bioinformatics/btt086`

   


.. conda:package:: quast

   |downloads_quast| |docker_quast|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>5.3.0-2</code>,  <code>5.3.0-1</code>,  <code>5.3.0-0</code>,  <code>5.2.0-4</code>,  <code>5.2.0-3</code>,  <code>5.2.0-2</code>,  <code>5.2.0-1</code>,  <code>5.2.0-0</code>,  <code>5.0.2-7</code>,  </span></summary>
      

      ``5.3.0-2``,  ``5.3.0-1``,  ``5.3.0-0``,  ``5.2.0-4``,  ``5.2.0-3``,  ``5.2.0-2``,  ``5.2.0-1``,  ``5.2.0-0``,  ``5.0.2-7``,  ``5.0.2-6``,  ``5.0.2-5``,  ``5.0.2-4``,  ``5.0.2-3``,  ``5.0.2-2``,  ``5.0.2-1``,  ``5.0.2-0``,  ``5.0.1-0``,  ``5.0.0-1``,  ``5.0.0-0``,  ``4.6.3-2``,  ``4.6.3-1``,  ``4.6.3-0``,  ``4.6.1-0``,  ``4.5-1``,  ``4.4-1``,  ``4.4-0``,  ``4.3-2``,  ``4.3-1``,  ``4.1-1``,  ``4.1-0``,  ``3.2-1``

      
      .. raw:: html

         </details>
      

   
   :depends bedtools: 
   :depends blast: ``>=2.16.0,<2.17.0a0``
   :depends bwa: 
   :depends circos: 
   :depends glimmerhmm: 
   :depends joblib: 
   :depends libgcc: ``>=13``
   :depends libstdcxx: ``>=13``
   :depends libzlib: ``>=1.3.1,<2.0a0``
   :depends matplotlib-base: 
   :depends minimap2: ``>=2.28,<3.0a0``
   :depends openjdk: ``>=11.0.1``
   :depends perl: ``>=5.32.1,<5.33.0a0 *_perl5``
   :depends python: ``>=3.13,<3.14.0a0``
   :depends python_abi: ``3.13.* *_cp313``
   :depends simplejson: 
   :requirements:

   :additional platforms:
      
      .. raw:: html

         <span class="additional-platforms"><code>linux-aarch64</code></span>
      

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/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 <https://mamba.readthedocs.io>`_ 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 quast

   and update with::

      mamba update quast

  To create a new environment, run::

      mamba create --name myenvname quast

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/quast:<tag>

   (see `quast/tags`_ for valid values for ``<tag>``)


.. |downloads_quast| image:: https://img.shields.io/conda/dn/bioconda/quast.svg?style=flat
   :target: https://anaconda.org/bioconda/quast
   :alt:   (downloads)
.. |docker_quast| image:: https://quay.io/repository/biocontainers/quast/status
   :target: https://quay.io/repository/biocontainers/quast
.. _`quast/tags`: https://quay.io/repository/biocontainers/quast?tab=tags


.. raw:: html

    <script>
        var package = "quast";
        var versions = ["5.3.0","5.3.0","5.3.0","5.2.0","5.2.0"];
    </script>





Notes
-----
\- GeneMark gene prediction software is disabled due to licensing issues



Download stats
-----------------

.. raw:: html
    :file: ../../templates/package_dashboard.html

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