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

.. title:: Package Recipe 'biopet-seqstat'
.. highlight: bash

biopet-seqstat
==============

.. conda:recipe:: biopet-seqstat
   :replaces_section_title:
   :noindex:

   SeqStat is a package that contains tools to generate stats from a FastQ file\, merge those stats for multiple samples\, and validate the generated stats files.

   :homepage: https://github.com/biopet/seqstat
   :license: MIT
   :recipe: /`biopet-seqstat <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopet-seqstat>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/biopet-seqstat/meta.yaml>`_

   SeqStat is a package that contains tools
   to generate stats from a FastQ file\,
   merge those stats for multiple samples\,
   and validate the generated stats files.

        
   \#\#\#\# Mode \- Generate

   Generate outputs several stats on a FASTQ file.

   Outputted stats\:

   \- Bases
      \- Total number
      \- Base qualities\, with the number of bases having that quality
      \- Number of each nucleotide
   \- Reads
      \- Total number
      \- minimum length
      \- maximum length
      \- A histogram of the average base qualities
      \- The quality encoding \(Sanger\, solexa etc.\)
      \- A histogram of the read lengths.
       
           

   \#\#\#\# Mode \- Merge

   This module will merge seqstat files together and keep the sample\/library\/readgroup structure.
   If required it\'s also possible to collapse this\, the output file then des not have any sample\/library\/readgroup structure.
       
           

   \#\#\#\# Mode \- Validate

   A file from SeqStat will validate the input files.
   If aggregation values can not be regenerated the file is considered corrupt.
   This should only happen when the user will edit the seqstat file manually.

   For documentation and manuals visit our github.io page\: https\:\/\/biopet.github.io\/seqstat


.. conda:package:: biopet-seqstat

   |downloads_biopet-seqstat| |docker_biopet-seqstat|

   :versions:
      
      

      ``1.0.1-1``,  ``1.0.1-0``,  ``1.0-1``,  ``1.0-0``,  ``0.1-2``,  ``0.1-1``,  ``0.1-0``

      

   
   :depends openjdk: ``>=8,<9``
   :depends python: 
   :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 biopet-seqstat

   and update with::

      mamba update biopet-seqstat

  To create a new environment, run::

      mamba create --name myenvname biopet-seqstat

  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/biopet-seqstat:<tag>

   (see `biopet-seqstat/tags`_ for valid values for ``<tag>``)


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


.. raw:: html

    <script>
        var package = "biopet-seqstat";
        var versions = ["1.0.1","1.0.1","1.0","1.0","0.1"];
    </script>





Notes
-----
biopet\-seqstat is a Java program that comes with a custom wrapper shell script. By default \'no default java option\' is set in the wrapper. The command that runs the program is \'biopet\-seqstat\'. If you want to overwrite it you can specify memory options directly after your binaries. If you have \_JAVA\_OPTIONS set globally this will take precedence. For example run it with \'biopet\-seqstat \-Xms512m \-Xmx1g\'. 


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/biopet-seqstat/README.html)

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