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

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

kcftools
========

.. conda:recipe:: kcftools
   :replaces_section_title:
   :noindex:

   Rapid method to screen for introgression using k\-mer counting

   :homepage: https://github.com/sivasubramanics/kcftools
   :license: GPL / GPL-3.0-only
   :recipe: /`kcftools <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/kcftools>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/kcftools/meta.yaml>`_

   KCFTOOLS is a Java\-based tool designed to identify genomic variations by analyzing k\-mer counts between
   reference and query sequences. The tool leverages k\-mer counting databases\, such as those generated by
   KMC\, to perform a variety of analyses\, including variation detection\, IBS window identification\, and
   genotype matrix generation.



.. conda:package:: kcftools

   |downloads_kcftools| |docker_kcftools|

   :versions:
      
      

      ``0.1.0-0``,  ``0.0.1-0``

      

   
   :depends kmc: ``>=3.2.0``
   :depends openjdk: ``17.*``
   :depends python: 
   :depends r-dplyr: 
   :depends r-ggforce: 
   :depends r-ggh4x: 
   :depends r-ggplot2: 
   :depends r-optparse: 
   :depends r-svglite: 
   :requirements:

   :additional platforms:
      

   .. 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 kcftools

   and update with::

      mamba update kcftools

  To create a new environment, run::

      mamba create --name myenvname kcftools

  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/kcftools:<tag>

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


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


.. raw:: html

    <script>
        var package = "kcftools";
        var versions = ["0.1.0","0.0.1"];
    </script>






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/kcftools/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/kcftools/README.html