SEQUANA
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    :alt: Documentation Status

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   :alt: JOSS (journal of open source software) DOI

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:Python version: 3.5 (and 2.7 without snakemake)
:Online documentation: `On readthedocs <http://sequana.readthedocs.org/>`_
:Issues and bug reports: `On github <https://github.com/sequana/sequana/issues>`_
:How to cite: For Sequana in general including the pipelines, please use 
    the `JOSS DOI (10.21105/joss.00352) <http://www.doi2bib.org/#/doi/10.21105/joss.00352>`_

    For the **genome coverage** tool (sequana_coverage):  Dimitri Desvillechabrol,
    Christiane Bouchier, Sean Kennedy, Thomas Cokelaer
    http://biorxiv.org/content/early/2016/12/08/092478

    For **Sequanix**: Dimitri Desvillechabrol, Rachel Legendre, Claire Rioualen,
    Christiane Bouchier, Jacques van Helden, Sean Kennedy, Thomas Cokelaer
    http://www.biorxiv.org/content/early/2017/07/12/162701
    DOI: https://doi.org/10.1101/162701


**Sequana** includes a set of pipelines related to NGS (new generation sequencing) including quality control, variant calling, coverage, taxonomy, transcriptomics. We also ship **Sequanix**, a graphical user interface for Snakemake pipelines. 

**Please see the** `documentation <http://sequana.readthedocs.org>`_ for an
up-to-date status and documentation.

