Metadata-Version: 1.2
Name: sequana-multitax
Version: 0.8.3
Summary: taxonomy, sequana, kraken, snakemake
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 **multitax** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
        
        :Overview: Runs taxonomic analysis on a set of samples using sequana_taxonomy (kraken behing the scene)
        :Input: A set of Fastq files
        :Output: HTML report for each sample and a summary HTML report for all (multiqc +  dendogram)
        :Status: draft
        :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_multitax
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_multitax --help
            sequana_pipelines_multitax --input-directory DATAPATH  --databases toydb
        
        For the database, you will need to provide your own databases. You can check out
        the documentation of kraken. The toydb here above is shipped wit sequana and
        should work for demo. See sequana_taxonomy standalone for more help and
        information. You can also checkout the sequana documentation (kraken module) 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd multitax
            sh multitax.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 multitax.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):
        
        - kraken
        - kraken2
        - sequana_taxonomy
        
        
        .. image::   https://github.com/sequana/sequana_multitax/raw/master/sequana_pipelines/multitax/dag.png
        
        Details
        ~~~~~~~~~
        
        This pipeline runs **sequana_taxonomy** (based on kraken) 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_multitax/master/sequana_pipelines/multitax/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
        ========= ====================================================================
        0.8.3     * add the confidence option in sequana_taxonomy rule
                  * improve html report
                  * uses new sequana framework to speed up --help calls
        0.8.2     * less stringent on requirements (mode warning)  
                  * fix input of the multiqc rule
        0.8.1     Fix requirements.
        0.8.0     **First release.**
        ========= ====================================================================
        
        
        
Keywords: taxonomy, sequana, kraken, snakemake
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
