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

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

clair
=====

.. conda:recipe:: clair
   :replaces_section_title:
   :noindex:

   Single\-molecule sequencing technologies have emerged in recent years and revolutionized structural variant calling\, complex genome assembly\, and epigenetic mark detection. However\, the lack of a highly accurate small variant caller has limited the new technologies from being more widely used. In this study\, we present Clair\, the successor to Clairvoyante\, a program for fast and accurate germline small variant calling\, using single molecule sequencing data. For ONT data\, Clair achieves the best precision\, recall and speed as compared to several competing programs\, including Clairvoyante\, Longshot and Medaka. Through studying the missed variants and benchmarking intentionally overfitted models\, we found that Clair may be approaching the limit of possible accuracy for germline small variant calling using pileup data and deep neural networks.

   :homepage: https://github.com/HKU-BAL/Clair
   :license: AGPLv3
   :recipe: /`clair <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clair>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clair/meta.yaml>`_

   


.. conda:package:: clair

   |downloads_clair| |docker_clair|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>2.1.1-1</code>,  <code>2.1.1-0</code>,  <code>2.1.0-1</code>,  <code>2.1.0-0</code>,  <code>2.0.7-0</code>,  <code>2.0.6-1</code>,  <code>2.0.6-0</code>,  <code>2.0.5-1</code>,  <code>2.0.5-0</code>,  </span></summary>
      

      ``2.1.1-1``,  ``2.1.1-0``,  ``2.1.0-1``,  ``2.1.0-0``,  ``2.0.7-0``,  ``2.0.6-1``,  ``2.0.6-0``,  ``2.0.5-1``,  ``2.0.5-0``,  ``2.0.4-0``,  ``2.0.3-0``,  ``2.0.2-0``,  ``2.0.1-0``,  ``2.0.0-0``

      
      .. raw:: html

         </details>
      

   
   :depends bcftools: 
   :depends intervaltree: 
   :depends matplotlib-base: 
   :depends numpy: ``>=1.17,<1.18``
   :depends parallel: 
   :depends pigz: 
   :depends pip: 
   :depends pypy3.6: 
   :depends pysam: 
   :depends python: ``>=3,<3.8``
   :depends python-blosc: 
   :depends samtools: 
   :depends tensorflow: ``>=1.13,<1.14``
   :depends vcflib: 
   :depends zstd: 
   :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 clair

   and update with::

      mamba update clair

  To create a new environment, run::

      mamba create --name myenvname clair

  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/clair:<tag>

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


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


.. raw:: html

    <script>
        var package = "clair";
        var versions = ["2.1.1","2.1.1","2.1.0","2.1.0","2.0.7"];
    </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/clair/README.html)

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