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

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

chewbbaca
=========

.. conda:recipe:: chewbbaca
   :replaces_section_title:
   :noindex:

   A complete suite for gene\-by\-gene schema creation and strain identification.

   :homepage: https://github.com/B-UMMI/chewBBACA
   :license: GPL3 / GPL-3.0-only
   :recipe: /`chewbbaca <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/chewbbaca>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/chewbbaca/meta.yaml>`_

   chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing \(wg\/cgMLST\) schemas\, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci.


.. conda:package:: chewbbaca

   |downloads_chewbbaca| |docker_chewbbaca|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.5.5-0</code>,  <code>2.5.4-0</code>,  <code>2.5.2-0</code>,  <code>2.5.1-0</code>,  <code>2.1.0-0</code>,  <code>2.0.17.2-0</code>,  <code>2.0.17.1-0</code>,  <code>2.0.16-0</code>,  <code>2.0.15-0</code>,  </span></summary>
      

      ``2.5.5-0``,  ``2.5.4-0``,  ``2.5.2-0``,  ``2.5.1-0``,  ``2.1.0-0``,  ``2.0.17.2-0``,  ``2.0.17.1-0``,  ``2.0.16-0``,  ``2.0.15-0``,  ``2.0.12-2``,  ``2.0.8-2``,  ``2.0.8-0``,  ``2.0.6-0``,  ``1.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends biopython: ``>=1.70``
   :depends blast: ``>=2.9.0``
   :depends clustalw: ``>=2.1``
   :depends mafft: 
   :depends numpy: ``>=1.14.0``
   :depends pandas: ``>=0.22.0``
   :depends plotly: ``>=1.12.9``
   :depends prodigal: ``>=2.6.0``
   :depends python: ``>=3``
   :depends requests: ``>=2.2.1``
   :depends scipy: ``>=0.13.3``
   :depends sparqlwrapper: ``>=1.8.0``
   :requirements:

   .. rubric:: Installation

   With an activated Bioconda channel (see :ref:`set-up-channels`), install with::

      conda install chewbbaca

   and update with::

      conda update chewbbaca

   or use the docker container::

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

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


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







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