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

.. title:: Package Recipe 'n50'
.. highlight: bash

n50
===

.. conda:recipe:: n50
   :replaces_section_title:
   :noindex:

   calculate N50 from FASTA\/FASTQ files\, producing both machine and human friendly outputs

   :homepage: http://metacpan.org/pod/Proch::N50
   :documentation: https://github.com/quadram-institute-bioscience/seqfu/wiki/n50
   
   :developer docs: https://github.com/quadram-institute-bioscience/seqfu/
   :license: mit
   :recipe: /`n50 <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/n50>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/n50/meta.yaml>`_
   :links: biotools: :biotools:`n50`, doi: :doi:`10.3390/bioengineering8050059`

   a program to calculate size metrics of a FASTA \(or FASTQ\) file\: minimum\, maximum\, average length\, N50\, N75\, N90 and the area of the Nx curve \(auN\).
   Gzipped files are supported as input\, and the output can be in compact\, csv\, tsv\, json or screen friendly format.



.. conda:package:: n50

   |downloads_n50| |docker_n50|

   :versions:
      
      
      .. raw:: html

         <details><summary><span class="truncated-version-list"><code>1.5.8-0</code>,  <code>1.5.6-0</code>,  <code>1.5.5-0</code>,  <code>1.5.4-0</code>,  <code>1.5.0-0</code>,  <code>1.4.10-1</code>,  <code>1.4.10-0</code>,  <code>1.4.2-2</code>,  <code>1.4.2-1</code>,  </span></summary>
      

      ``1.5.8-0``,  ``1.5.6-0``,  ``1.5.5-0``,  ``1.5.4-0``,  ``1.5.0-0``,  ``1.4.10-1``,  ``1.4.10-0``,  ``1.4.2-2``,  ``1.4.2-1``,  ``1.4.2-0``,  ``1.4.1-0``,  ``1.3.0-1``,  ``1.3.0-0``,  ``1.2.0-0``,  ``1.0.0-0``,  ``0.92-0``,  ``0.90-0``,  ``0.83-0``,  ``0.82-0``,  ``0.80-0``,  ``0.60-3``,  ``0.60-2``,  ``0.60-1``,  ``0.60-0``

      
      .. raw:: html

         </details>
      

   
   :depends perl: ``>=5.32.1,<6.0a0 *_perl5``
   :depends perl-exporter: 
   :depends perl-fastx-reader: ``>=1.8.0``
   :depends perl-file-which: 
   :depends perl-getopt-long: 
   :depends perl-json-pp: 
   :depends perl-perlio-encoding: 
   :depends perl-pod-usage: 
   :depends perl-text-asciitable: 
   :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 n50

   and update with::

      mamba update n50

  To create a new environment, run::

      mamba create --name myenvname n50

  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/n50:<tag>

   (see `n50/tags`_ for valid values for ``<tag>``)


.. |downloads_n50| image:: https://img.shields.io/conda/dn/bioconda/n50.svg?style=flat
   :target: https://anaconda.org/bioconda/n50
   :alt:   (downloads)
.. |docker_n50| image:: https://quay.io/repository/biocontainers/n50/status
   :target: https://quay.io/repository/biocontainers/n50
.. _`n50/tags`: https://quay.io/repository/biocontainers/n50?tab=tags


.. raw:: html

    <script>
        var package = "n50";
        var versions = ["1.5.8","1.5.6","1.5.5","1.5.4","1.5.0"];
    </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/n50/README.html)

.. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
   :target: http://bioconda.github.io/recipes/n50/README.html