Metadata-Version: 2.1
Name: sequana
Version: 0.14.5
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/0.14.5.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=main
            :target: https://github.com/sequana/sequana/actions/workflows/main.yml
        
        .. image:: https://coveralls.io/repos/github/sequana/sequana/badge.svg?branch=main
            :target: https://coveralls.io/github/sequana/sequana?branch=main
        
        .. image:: http://readthedocs.org/projects/sequana/badge/?version=main
            :target: http://sequana.readthedocs.org/en/latest/?badge=main
            :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: 15 35 20 15 15
            :header-rows: 1
        
            * - **name/github**
              - **description**
              - **Latest Pypi version**
              - **Test passing**
              - **apptainers**
            * - `sequana_pipetools <https://github.com/sequana/sequana_pipetools>`_
              - Create and Manage Sequana pipeline
              - .. 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
              -  
            * - `sequana-wrappers <https://github.com/sequana/sequana-wrappers>`_
              - Set of wrappers to build pipelines
              - 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
              -
            * - `demultiplex <https://github.com/sequana/demultiplex>`_
              - Demultiplex your raw data
              - .. 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
              -
            * - `denovo <https://github.com/sequana/denovo>`_
              - denovo sequencing data
              - .. image:: https://badge.fury.io/py/sequana-denovo.svg
                    :target: https://pypi.python.org/pypi/sequana-denovo
              - .. image:: https://github.com/sequana/denovo/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/denovo/actions/workflows/main.yml
              - .. image:: https://github.com/sequana/denovo/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/denovo/actions/workflows/apptainer.yml
            * - `fastqc <https://github.com/sequana/fastqc>`_
              - Get Sequencing Quality control
              - .. 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
              - .. image:: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/fastqc/actions/workflows/apptainer.yml
            * - `mapper <https://github.com/sequana/mapper>`_
              - Map sequences on target genome
              - .. 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
              - .. image:: https://github.com/sequana/mapper/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/mapper/actions/workflows/apptainer.yml
            * - `pacbio_qc <https://github.com/sequana/pacbio_qc>`_
              - Pacbio quality control
              - .. 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
              - .. image:: https://github.com/sequana/pacbio_qc/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/pacbio_qcr/actions/workflows/apptainer.yml
            * - `ribofinder <https://github.com/sequana/ribofinder>`_
              - Find ribosomal content
              - .. 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
              - .. image:: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/ribofinder/actions/workflows/apptainer.yml
            * - `rnaseq <https://github.com/sequana/rnaseq>`_
              - RNA-seq analysis 
              - .. 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
              - .. image:: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/rnaseq/actions/workflows/apptainer.yml
            * - `variant_calling <https://github.com/sequana/variant_calling>`_
              - 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
              - .. image:: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/variant_calling/actions/workflows/apptainer.yml
            * - `multicov <https://github.com/sequana/multicov>`_
              - Coverage (mapping)
              - .. image:: https://badge.fury.io/py/sequana-multicov.svg
                    :target: https://pypi.python.org/pypi/sequana-multicov
              - .. image:: https://github.com/sequana/multicov/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/multicov/actions/workflows/main.yml
              - .. image:: https://github.com/sequana/coverage/actions/workflows/apptainer.yml/badge.svg
                    :target: https://github.com/sequana/coverage/actions/workflows/apptainer.yml
            * - `laa <https://github.com/sequana/laa>`_
              - Long read Amplicon Analysis
              - .. image:: https://badge.fury.io/py/sequana-laa.svg
                    :target: https://pypi.python.org/pypi/sequana-laa
              - .. image:: https://github.com/sequana/laa/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/laa/actions/workflows/main.yml
              -
            * - `revcomp <https://github.com/sequana/revcomp>`_
              - reverse complement of sequence data
              - .. image:: https://badge.fury.io/py/sequana-revcomp.svg
                    :target: https://pypi.python.org/pypi/sequana-revcomp
              - .. image:: https://github.com/sequana/revcomp/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/revcomp/actions/workflows/main.yml
              -
            * - `downsampling <https://github.com/sequana/downsampling>`_
              - downsample sequencing data
              - .. image:: https://badge.fury.io/py/sequana-downsampling.svg
                    :target: https://pypi.python.org/pypi/sequana-downsampling
              - .. image:: https://github.com/sequana/downsampling/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/downsampling/actions/workflows/main.yml
              -
        
        
        
        .. list-table:: Pipelines not yet released 
            :widths: 20 40 20 20 
            :header-rows: 1
        
            * - **name/github**
              - **description**
              - **Latest Pypi version**
              - **Test passing**
            * - `trf <https://github.com/sequana/trf>`_
              - Find repeats
              - .. image:: https://badge.fury.io/py/sequana-trf.svg
                    :target: https://pypi.python.org/pypi/sequana-trf
              - .. image:: https://github.com/sequana/trf/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/trf/actions/workflows/main.yml
            * - `multitax <https://github.com/sequana/multitax>`_
              - Taxonomy analysis
              - .. image:: https://badge.fury.io/py/sequana-multitax.svg
                    :target: https://pypi.python.org/pypi/sequana-multitax
              - .. image:: https://github.com/sequana/multitax/actions/workflows/main.yml/badge.svg
                    :target: https://github.com/sequana/multitax/actions/workflows/main.yml
        
        **Please see the** `documentation <http://sequana.readthedocs.org>`_ for an
        up-to-date status and documentation.
        
        
        Contributors
        ============
        
        Maintaining Sequana 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
        ========= ==========================================================================
        0.14.5    * move start_pipeline standalone in 
                    https://github.com/sequana/sequana_pipetools
                  * update snpeff module to allows build command to have options
        0.14.4    * hotfix bug on kegg colorised pathways
                  * Fix the hover_name in rnadiff volcano plot to include the
                    index/attribute.
                  * pin snakemake to be >=7.16
        0.14.3    * new fisher metric in variant calling
                  * ability to use several feature in rnaseq/rnadiff
                  * pin several libaries due to regression during installs
        0.14.2    * Update ribodesigner 
        0.14.1    * Kegg enrichment: add gene list 'all' and fix incomplete annotation case
                  * New uniprot module for GO term enrichment and enrichment
                    refactorisation (transparent for users)
        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
