Metadata-Version: 1.2
Name: sequana-mapper
Version: 0.8.7
Summary: A simple mapper to map reads onto a reference. This is useful for quick QCs and also secondary analysis
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: This is is the **mapper** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: This is a simple pipeline to map several FastQ files onto a reference using different mappers/aligners
        :Input: A set of FastQ files.
        :Output: A set of BAM files (and/or bigwig)
        :Status: Production
        :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_mapper
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_mapper --help
            sequana_pipelines_mapper --input-directory DATAPATH 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd mapper
            sh mapper.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 mapper.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):
        
        - bamtools
        - bwa
        - multiqc
        - sequana_coverage
        - minimap2
        - bowtie2
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_mapper/master/sequana_pipelines/mapper/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs **mapper** 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_mapper/master/sequana_pipelines/mapper/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
        ========= ====================================================================
        0.8.7     * fix config file creation (for bigwig)
        0.8.6     * added bowtie2 mapper + bigwig as output, make coverage optional
        0.8.5     * create a sym link to the HTML report. Better post cleaning.
        0.8.4     * Fixing multiqc (synchronized with sequana updates) 
        0.8.3     * add sequana_coverage rule. 
        0.8.2     * add minimap2 mapper 
        0.8.1     * fix bamtools stats rule to have different output name for multiqc
        0.8.0     **First release.**
        ========= ====================================================================
        
        
Keywords: snakemake, sequana, bwa, bowtie2, minimap2
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 4 - Beta
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
