:orphan:

Gallery
==========

General-purpose examples for sequana library. The following examples illustrates
how Sequana library itself can be used to read and create some plots used within
the pipelines.


.. raw:: html

  <div id='sg-tag-list' class='sphx-glr-tag-list'></div>


.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

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    <div class="sphx-glr-thumbcontainer" tooltip="Quality histogram a la fastQC">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_fastqc_hist_thumb.png
    :alt:

  :doc:`/auto_examples/plot_fastqc_hist`

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      <div class="sphx-glr-thumbnail-title">Quality histogram a la fastQC</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="QC pacbio example">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_qc_pacbio_thumb.png
    :alt:

  :doc:`/auto_examples/plot_qc_pacbio`

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      <div class="sphx-glr-thumbnail-title">read length histograms pacbio data</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Plot histogram of MAPQ values contained in a BAM file">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_bam_thumb.png
    :alt:

  :doc:`/auto_examples/plot_bam`

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      <div class="sphx-glr-thumbnail-title">BAM module example</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Coverage module example">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_coverage_thumb.png
    :alt:

  :doc:`/auto_examples/plot_coverage`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Coverage module example</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In Sequana, we provide tools to quickly assess the taxonomic content of a reads (FastQ). It is based on the Kraken and Krona software. Sequana bridges the gap between those tools, Kraken databases and a simple interface to get a quick taxonomic overview of the FastQ content.">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_kraken_thumb.png
    :alt:

  :doc:`/auto_examples/plot_kraken`

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      <div class="sphx-glr-thumbnail-title">Kraken module example</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Pipeline statistics">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_pipeline_stats_thumb.png
    :alt:

  :doc:`/auto_examples/plot_pipeline_stats`

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      <div class="sphx-glr-thumbnail-title">Pipeline statistics</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Plot running median on a data set">

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  .. image:: /auto_examples/images/thumb/sphx_glr_plot_running_median_thumb.png
    :alt:

  :doc:`/auto_examples/plot_running_median`

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      <div class="sphx-glr-thumbnail-title">Running median example</div>
    </div>


.. thumbnail-parent-div-close

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    </div>


.. toctree::
   :hidden:

   /auto_examples/plot_fastqc_hist
   /auto_examples/plot_qc_pacbio
   /auto_examples/plot_bam
   /auto_examples/plot_coverage
   /auto_examples/plot_kraken
   /auto_examples/plot_pipeline_stats
   /auto_examples/plot_running_median


.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-gallery

    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download all examples in Python source code: auto_examples_python.zip </auto_examples/auto_examples_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: auto_examples_jupyter.zip </auto_examples/auto_examples_jupyter.zip>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_