Metadata-Version: 2.1
Name: sequana
Version: 0.14.0
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/0.14.0.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, 3.9
        :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.
        
        
        
        .. list-table:: Pipelines and tools available in the Sequana project
            :widths: 20 40 40
            :header-rows: 1
        
            * - **pipeline or tools**
              - **Latest Pypi version**
              - **Test passing**
            * - https://github.com/sequana/sequana_pipetools
              - .. image:: https://badge.fury.io/py/sequana-pipetools.svg
                    :target: https://pypi.python.org/pypi/sequana_pipetools
              - .. image:: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/sequana_pipetools/actions/workflows/main.yml
            * - https://github.com/sequana/sequana-wrappers
              - Not on pypi
              - .. image:: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/sequana-wrappers/actions/workflows/main.yml
            * - https://github.com/sequana/demultiplex
              - .. image:: https://badge.fury.io/py/sequana-demultiplex.svg
                    :target: https://pypi.python.org/pypi/sequana-demultiplex
              - .. image:: https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/demultiplex/actions/workflows/main.yml
            * - https://github.com/sequana/fastqc
              - .. image:: https://badge.fury.io/py/sequana-fastqc.svg
                    :target: https://pypi.python.org/pypi/sequana-fastqc
              - .. image:: https://github.com/sequana/fastqc/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/fastqc/actions/workflows/main.yml
            * - https://github.com/sequana/mapper
              - .. image:: https://badge.fury.io/py/sequana-mapper.svg
                    :target: https://pypi.python.org/pypi/sequana-mapper
              - .. image:: https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/mapper/actions/workflows/main.yml
            * - https://github.com/sequana/pacbio_qc
              - .. image:: https://badge.fury.io/py/sequana-pacbio-qc.svg
                    :target: https://pypi.python.org/pypi/sequana-pacbio-qc
              - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/pacbio_qc/actions/workflows/main.yml
            * - https://github.com/sequana/ribofinder
              - .. image:: https://badge.fury.io/py/sequana-ribofinder.svg
                    :target: https://pypi.python.org/pypi/sequana-ribofinder
              - .. image:: https://github.com/sequana/ribofinder/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/ribofinder/actions/workflows/main.yml
            * - https://github.com/sequana/rnaseq
              - .. image:: https://badge.fury.io/py/sequana-rnaseq.svg
                    :target: https://pypi.python.org/pypi/sequana-rnaseq
              - .. image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/rnaseq/actions/workflows/main.yml
            * - https://github.com/sequana/variant_calling
              - .. image:: https://badge.fury.io/py/sequana-variant-calling.svg
                    :target: https://pypi.python.org/pypi/sequana-variant-calling
              - .. image:: https://github.com/sequana/variant_calling/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/variant_calling/actions/workflows/main.yml
        
        **Please see the** `documentation <http://sequana.readthedocs.org>`_ for an
        up-to-date status and documentation.
        
        
        Contributors
        ============
        
        Maintaining BioServices would not have been possible without users and contributors. 
        Each contribution has been an encouragement to pursue this project. Thanks to all:
        
        .. image:: https://contrib.rocks/image?repo=sequana/sequana
            :target: https://github.com/sequana/sequana/graphs/contributors
        
        
        
        Changelog
        ~~~~~~~~~
        
        ========= ========================================================================
        Version   Description
        ========= ========================================================================
        0.14.0    * pinned click>=8.1.0 due to API change (autocomplete)
                  * moved tests around to decrease packaging from 16 to 4Mb
                  * ribodesigner: new plots, clustering and notebook         
        0.13.X    * Remove useless standalones or moved to main **sequana** command
                  * Move sequana_lane_merging into a subcommand (sequana lane_merging)
                  * General cleanup of documentation, test and links to pipelines
                  * add new ribodesigner subcommand
        0.12.7    * Fix memory leak in len() of FastA class
        0.12.6    * remove some rules now in https://github.com/sequana/sequana-wrappers
        0.12.5    * refactorisation of VCF tools/modules to use vcfpy instead of pyVCF
        0.12.4    * complete change log before 0.12.4 on readthedocs.org
        ========= ========================================================================
        
        
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 :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
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
Provides-Extra: testing
Provides-Extra: pipelines
Provides-Extra: doc
