Metadata-Version: 1.1
Name: ddrage
Version: 1.2.0
Summary: Simulator for ddRADseq (double digest restriction site associdated DNA squencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).
Home-page: https://bitbucket.org/genomeinformatics/rage
Author: Henning Timm
Author-email: henning.timm@uni-due.de
License: MIT
Description: RAGE - ddRAD Data Generator
        ============================
        
        RAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads.
        The generated datasets can be used to test ddRAD analysis tools and validate their results.
        
        The documentation, including a tutorial, can be found `here <https://ddrage.readthedocs.io/>`_.
        The code is hosted on `bitbucket`_, `PyPI`_, and `bioconda`_.
        
        .. _bitbucket: https://bitbucket.org/genomeinformatics/rage
        .. _PyPI: https://pypi.python.org/pypi/ddrage/
        .. _bioconda: https://bioconda.github.io/recipes/ddrage/README.html
        
        System Requirements
        ~~~~~~~~~~~~~~~~~~~
        
        - python >= 3.5
        - numba
        - numpy
        - matplotlib
        - pyyaml
        - scipy
        
        
        For the docs:
        
        - sphinx
        - sphinx_rtd_theme
        
        For parameter visualization:
        
        - bokeh
        
        
        Installation
        ~~~~~~~~~~~~
        
        We recommend the installation using conda:
        
        .. code-block:: shell
        
           $ conda create -c bioconda -n rage  python rage
           $ source activate rage
        
        Alternatively, you can download the source code from `bitbucket`_ and install it using the setup script:
        
        .. code-block:: shell
        
           $ git clone https://bitbucket.org/genomeinformatics/rage.git
           $ cd rage
           /rage$ python setup.py install
        
        In this case you have to install the requirements listed above.
        
        
        .. _bitbucket: https://bitbucket.org/genomeinformatics/rage
        
        
        Usage
        ~~~~~
        
        To simulate a ddRAD dataset, call rage from the command line:
        
        .. code-block:: shell
        
           $ rage
        
        you can specify parameters to change dataset parameters such as number of individuals (``-n``), nr of loci (``-l``), and coverage (``--coverage``):
        
        .. code-block:: shell
        
           $ rage -n 6 -l 10000 --coverage 30
        
        This creates a dataset with reads from 6 individuals at 10000 loci with an expected coverage of 30.
        
        A more detialed tutorial can be found `here`_.
        
        .. _here: https://ddrage.readthedocs.io/en/latest/getting-started/
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
