Metadata-Version: 2.1
Name: sequana_laa
Version: 0.9.0
Summary: Long read amplicon 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: 
        .. image:: https://badge.fury.io/py/sequana-laa.svg
             :target: https://pypi.python.org/pypi/sequana_laa
        
        .. 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/laa/actions/workflows/main.yml/badge.svg
           :target: https://github.com/sequana/laa/actions/workflows/main.yml)
        
        
        
        This is is the **laa** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ project
        
        :Overview: Perform amplicon analysis on Pacbio data sets including variant and phylogeny
        :Input: A set of CCS files from pacbio in FastQ formats
        :Output: variant calling, phylogney, consensus genomes, etc
        :Status: production but may change
        :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
        
        This pipeline was used in :
        
        - L'Honneur et al (polyomavirus, 2022) https://pubmed.ncbi.nlm.nih.gov/34979561/ 
        - Kali et al (rabies,2021), https://pubmed.ncbi.nlm.nih.gov/33444703/
        - Claireaux et al. (gene involved in HIV, 2022) accepted, not yet on pubmed
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_laa
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_laa --help
            sequana_laa --input-directory DATAPATH 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd laa
            sh laa.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 laa.rules -c config.yaml --cores 4 --stats stats.txt --wrapper-prefix git+file:///home/cokelaer/Work/github/forked/sequana-wrappers
        
        Or use `sequanix <https://sequana.readthedocs.io/en/main/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - vt
        - freebayes
        - igvtools
        - sequana
        - snpeff (optional)
        - samtools
        - bamtools
        - minimap2
        
        .. image:: https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/dag.png
        
        
        Details
        ~~~~~~~~~
        
        This pipeline runs amplicon analysis on long reads data from pacbio sequencers. 
        
        
        Rules and configuration details
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Here is the `latest documented configuration file <https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/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     add singularity containers
        0.8.0     **First release.**
        ========= ====================================================================
        
        
        
Keywords: Snakemake, Sequana, Amplicon, Variant calling, phylogeny
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 :: 3.7
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
Description-Content-Type: text/x-rst
