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

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

biodiff
=======

.. conda:recipe:: biodiff
   :replaces_section_title:
   :noindex:

   exact comparison of biological sequences

   :homepage: https://gitlab.com/LPCDRP/biodiff
   :license: GPLv3+
   :recipe: /`biodiff <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biodiff>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biodiff/meta.yaml>`_

   biodiff is a variant caller that determines the exact differences between two biological sequences. It can operate on DNA and protein sequences\, as long as they are in fasta format. The sequences to be compared must have the same fasta header \(up to the first whitespace\). If the reference and query each have only one sequence\, however\, the header need not match and the comparison will be done\, but a warning will be emitted. Output is in the Variant Call Format.


.. conda:package:: biodiff

   |downloads_biodiff| |docker_biodiff|

   :versions:
      
      

      ``0.2.2-5``,  ``0.2.2-4``,  ``0.2.2-3``,  ``0.2.2-2``,  ``0.2.2-1``,  ``0.2.2-0``

      

   
   :depends libgcc-ng: ``>=12``
   :depends perl: 
   :requirements:

   .. 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 biodiff

   and update with::

      mamba update biodiff

  To create a new environment, run::

      mamba create --name myenvname biodiff

  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/biodiff:<tag>

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


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


.. raw:: html

    <script>
        var package = "biodiff";
        var versions = ["0.2.2","0.2.2","0.2.2","0.2.2","0.2.2"];
    </script>






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

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

Link to this page
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Render an |install-with-bioconda| badge with the following MarkDown::

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.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
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