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

.. title:: Package Recipe 'clair3-trio'
.. highlight: bash

clair3-trio
===========

.. conda:recipe:: clair3-trio
   :replaces_section_title:
   :noindex:

   Clair3\-Trio is a variants caller tailored for family trios from nanopore long\-reads. Clair3\-Trio employs a Trio\-to\-Trio deep neural network model that allows it to input all trio’s sequencing information and output all trio’s predicted variants within a single model\, to perform far better variant calling. We also present MCVLoss\, the first loss function that can improve variants calling in trios by leveraging the explicitly encoding of the priors of the Mendelian inheritance in trios. Clair3\-Trio showed comprehensive improvement in experiments. It predicted much fewer Mendelian inheritance violation variations than current state\-of\-the\-art methods.

   :homepage: https://github.com/HKU-BAL/Clair3-Trio
   :license: BSD-3-Clause
   :recipe: /`clair3-trio <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clair3-trio>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/clair3-trio/meta.yaml>`_

   


.. conda:package:: clair3-trio

   |downloads_clair3-trio| |docker_clair3-trio|

   :versions:
      
      

      ``0.7-0``,  ``0.6-1``,  ``0.6-0``,  ``0.5-0``,  ``0.3-2``,  ``0.3-1``,  ``0.3-0``,  ``0.2-0``,  ``0.1-0``

      

   
   :depends bzip2: ``>=1.0.8,<2.0a0``
   :depends cffi: 
   :depends libgcc-ng: ``>=12``
   :depends libstdcxx-ng: ``>=12``
   :depends libzlib: ``>=1.2.13,<1.3.0a0``
   :depends numpy: 
   :depends parallel: ``20191122.*``
   :depends pigz: 
   :depends pypy3.6: 
   :depends pytables: 
   :depends python: ``>=3.9,<3.10.0a0``
   :depends python_abi: ``3.9.* *_cp39``
   :depends samtools: ``1.15.1.*``
   :depends tensorflow: ``2.8.0.*``
   :depends whatshap: ``1.7.*``
   :depends xz: ``>=5.2.6,<6.0a0``
   :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 clair3-trio

   and update with::

      mamba update clair3-trio

  To create a new environment, run::

      mamba create --name myenvname clair3-trio

  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/clair3-trio:<tag>

   (see `clair3-trio/tags`_ for valid values for ``<tag>``)


.. |downloads_clair3-trio| image:: https://img.shields.io/conda/dn/bioconda/clair3-trio.svg?style=flat
   :target: https://anaconda.org/bioconda/clair3-trio
   :alt:   (downloads)
.. |docker_clair3-trio| image:: https://quay.io/repository/biocontainers/clair3-trio/status
   :target: https://quay.io/repository/biocontainers/clair3-trio
.. _`clair3-trio/tags`: https://quay.io/repository/biocontainers/clair3-trio?tab=tags


.. raw:: html

    <script>
        var package = "clair3-trio";
        var versions = ["0.7","0.6","0.6","0.5","0.3"];
    </script>






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-----------------

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

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