Metadata-Version: 1.2
Name: sequana
Version: 0.12.1
Summary: A set of standalone application and pipelines dedicated to NGS (new generation sequencing) analysis
Home-page: http://github.com/sequana/sequana
Author: Thomas Cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Download-URL: https://github.com/sequana/sequana/archive/0.12.1.tar.gz
Description: SEQUANA
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        .. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)
           :target: http://bioconda.github.io/recipes/sequana/README.html
        
        .. image:: https://badge.fury.io/py/sequana.svg
            :target: https://pypi.python.org/pypi/sequana
        
        .. image:: https://github.com/sequana/sequana/actions/workflows/main.yml/badge.svg?branch=master
            :target: https://github.com/sequana/sequana/actions/workflows/main.yml
        
        .. image:: https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=master
            :target: https://coveralls.io/github/sequana/sequana?branch=master
        
        .. image:: http://readthedocs.org/projects/sequana/badge/?version=master
            :target: http://sequana.readthedocs.org/en/latest/?badge=master
            :alt: Documentation Status
        
        .. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg
           :target: http://joss.theoj.org/papers/10.21105/joss.00352
           :alt: JOSS (journal of open source software) DOI
        
        
        :Python version: 3.7, 3.8
        :Documentation: `On readthedocs <http://sequana.readthedocs.org/>`_
        :Issues: `On github <https://github.com/sequana/sequana/issues>`_
        :How to cite: Citations are important for us to carry on developments.
            For Sequana library (including the pipelines), please use
        
            Cokelaer et al, (2017), 'Sequana': a Set of Snakemake NGS pipelines, Journal of
            Open Source Software, 2(16), 352, `JOSS DOI doi:10.21105/joss.00352 <https://joss.theoj.org/papers/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.
            Sequanix: A Dynamic Graphical Interface for Snakemake Workflows
            Bioinformatics, bty034, https://doi.org/10.1093/bioinformatics/bty034
            Also available on bioRxiv (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.
        
        +------------------------------------------------+--------------------------+-----------------------+
        | **pipeline or tools**                          | **Latest Pypi verison**  |  **Test passing**     |
        +------------------------------------------------+--------------------------+-----------------------+
        | https://github.com/sequana/sequana_pipetools   |     |pipetools_pypi|     | |pipetools_test|      |
        +------------------------------------------------+--------------------------+-----------------------+
        | https://github.com/sequana/sequana-wrappers    |        not on pypi       | |wrappers_test|       |
        +------------------------------------------------+--------------------------+-----------------------+
        | https://github.com/sequana/fastqc              |         |fastqc_pypi|    |  |fastqc_test|        |
        +------------------------------------------------+--------------------------+-----------------------+
        | https://github.com/sequana/ribofinder          |         |ribo_pypi|      |  |ribo_test|          |
        +------------------------------------------------+--------------------------+-----------------------+
        
        
        .. |pipetools_pypi| image:: https://badge.fury.io/py/sequana-pipetools.svg
            :target: https://pypi.python.org/pypi/sequana_pipetools
        
        .. |pipetools_test| image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg?branch=master
            :target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml
        
        .. |wrappers_test| image:: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg
            :target: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml
        
        .. |fastqc_pypi| image:: https://badge.fury.io/py/sequana-fastqc.svg
            :target: https://pypi.python.org/pypi/sequana-fastqc
        
        .. |fastqc_test| image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg?branch=master
            :target: https://github.com/sequana/fastqc/actions/workflows/main.yml
        
        .. |ribo_pypi| image:: https://badge.fury.io/py/sequana-ribofinder.svg
            :target: https://pypi.python.org/pypi/sequana-ribofinder
        
        .. |ribo_test| image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg?branch=master
            :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
        
        
        **Please see the** `documentation <http://sequana.readthedocs.org>`_ for an
        up-to-date status and documentation.
        
        
Keywords: NGS,snakemake
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
