Metadata-Version: 1.2
Name: sequana-quality-control
Version: 0.9.0
Summary: A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants
Home-page: https://github.com/sequana/
Author: thomas cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: thomas cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: 
        .. image:: https://badge.fury.io/py/sequana-quality-control.svg
             :target: https://pypi.python.org/pypi/sequana_quality_control
        
        .. 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
        
        .. image:: https://github.com/sequana/quality_control/actions/workflows/main.yml/badge.svg
           :target: https://github.com/sequana/quality_control/actions/workflows    
        
        
        This pipeline is not maintained anymore but should be functional. It is a short-read quality control pipeline
        from the `Sequana <https://sequana.readthedocs.org>`_ project. We would recommend to use the fastqc, demultiplex,
        and multitax pipelines instead.
        
        :Overview: A quality control pipeline for illumina data set. This pipeline removes contaminants (e.g. Phix), performs fastqc, adapter cleaning and trimming and checks for contaminants
        :Input: Raw fastq files
        :Output: Cleaned fastQ files, remove phix and adapters + taxonomy
        :Status: production. **not maintained**. Please use sequana_fastqc and sequana_multitax pipeline instead
        :Citation: 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
        
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_quality_control
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_quality_control --help
            sequana_quality_control --input-directory DATAPATH 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd quality_control
            sh quality_control.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can 
        retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s quality_control.rules -c config.yaml --cores 4 --stats stats.txt
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - fastqc
        - bwa
        - kraken2 (optional)
        - krona (optional)
        - sambamba
        - samtools
        - pigz
        - cutadapt [or atropos]
        
        .. image:: https://raw.githubusercontent.com/sequana/quality_control/master/sequana_pipelines/quality_control/dag.png
        
        
        Details
        ~~~~~~~
        
        This pipeline runs **quality_control** in parallel on the input fastq files (paired or not). 
        A brief sequana summary report is also produced.
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/sequana_quality_control/master/sequana_pipelines/quality_control/config.yaml>`_
        to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. 
        
        ChangeLog
        ~~~~~~~~~
        
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        0.9.0     * remove design_file for cutadapt to reflect changes in
                    sequana 0.12.0 
                  * update kraken rules to use a kraken2 version
                  * Update to use new sequana framework (0.12)
                  * added CI action
        0.8.4     * fix the onsuccess section to reflect changes in sequana 0.9.3
        0.8.3     * fix cleaning output files
        0.8.2     * fix typo in parameter (-skip-phix-removal --> --skip-phix-removal)
                  * implement hiearchical kraken analysis. Required major updates of
                    the sequana kraken rules + general fixes in sequana
        0.8.1     uses more sequana tools to handle the options
        ========= ====================================================================
        
Keywords: snakemake, NGS, sequana, denovo, assembly, short read
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
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
