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Sequana: a set of Snakemake NGS pipelines

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SEQUANA ############

.. 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/demultiplex | |demultiplex_pypi| | |demultiplex_test| | +------------------------------------------------+--------------------------+-----------------------+ | https://github.com/sequana/fastqc | |fastqc_pypi| | |fastqc_test| | +------------------------------------------------+--------------------------+-----------------------+ | https://github.com/sequana/mapper | |mapper_pypi| | |mapper_test| | +------------------------------------------------+--------------------------+-----------------------+ | https://github.com/sequana/ribofinder | |ribo_pypi| | |ribo_test| | +------------------------------------------------+--------------------------+-----------------------+ | https://github.com/sequana/rnaseq | |rnaseq_pypi| | |rnaseq_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

.. |mapper_pypi| image:: https://badge.fury.io/py/sequana-mapper.svg :target: https://pypi.python.org/pypi/sequana-mapper

.. |mapper_test| image:: https://github.com/sequana/mapper/actions/workflows/main.yml/badge.svg?branch=master :target: https://github.com/sequana/mapper/actions/workflows/main.yml

.. |demultiplex_pypi| image:: https://badge.fury.io/py/sequana-demultiplex.svg :target: https://pypi.python.org/pypi/sequana-demultiplex

.. |demultiplex_test| image:: https://github.com/sequana/demultiplex/actions/workflows/main.yml/badge.svg?branch=master :target: https://github.com/sequana/demultiplex/actions/workflows/main.yml

.. |rnaseq_pypi| image:: https://badge.fury.io/py/sequana-rnaseq.svg :target: https://pypi.python.org/pypi/sequana-rnaseq

.. |rnaseq_test| image:: https://github.com/sequana/rnaseq/actions/workflows/main.yml/badge.svg?branch=master :target: https://github.com/sequana/rnaseq/actions/workflows/main.yml

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

Changelog


========= ====================================================================
Version   Description
========= ====================================================================
0.12.4    * complete change log before 0.12.4 on readthedocs.org
========= ====================================================================

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