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        "author": "Henning Timm",
        "author_email": "henning.timm@uni-due.de",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Medical Science Apps."
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        "description": "#############################\nddRAGE - ddRAD Data Generator\n#############################\n\n\nddRAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads.\nThe generated data sets can be used to test ddRAD analysis tools and validate their results.\n\nThe documentation, including a tutorial, can be found `here <https://ddrage.readthedocs.io/>`_.\nThe code is hosted on `bitbucket`_, `PyPI`_, and `bioconda`_.\n\n.. _bitbucket: https://bitbucket.org/genomeinformatics/rage\n.. _PyPI: https://pypi.python.org/pypi/ddrage/\n.. _bioconda: https://bioconda.github.io/recipes/ddrage/README.html\n\n\n*******************\nSystem Requirements\n*******************\n\n- python >= 3.5\n- numba\n- numpy\n- matplotlib\n- pyyaml\n- scipy\n\n\nFor the docs:\n\n- sphinx\n\nFor parameter visualization:\n\n- bokeh\n\n\n************\nInstallation\n************\n\nWe recommend the installation using conda:\n\n.. code-block:: shell\n\n   $ conda create -n ddrage -c bioconda ddrage\n   $ source activate ddrage\n\nAlternatively, you can download the source code from `bitbucket`_ and install it using the setup script:\n\n.. code-block:: shell\n\n   $ git clone https://bitbucket.org/genomeinformatics/rage.git ddrage\n   $ cd ddrage\n   /rage$ python setup.py install\n\nIn this case you have to install the requirements listed above.\n\n\n*****\nUsage\n*****\n\nTo simulate a ddRAD data set, call ddrage from the command line:\n\n.. code-block:: shell\n\n   $ ddrage\n\nyou can specify parameters to change data set parameters such as number of individuals (``-n``), nr of loci (``-l``), and coverage (``--coverage``):\n\n.. code-block:: shell\n\n   $ ddrage -n 6 -l 10000 --coverage 30\n\nThis creates a data set with reads from 6 individuals at 10000 loci with an expected coverage of 30.\n\nA more detailed tutorial can be found `on readthedocs <https://ddrage.readthedocs.io/en/latest/getting-started/>`_.\n\n\n*************\nCiting ddRAGE\n*************\n\nOur paper describing ddRAGE has been published in `Molecular Ecology Resources <http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12743/full>`_.\nYou can cite it as follows:\n\n.. code-block:: text\n\n    Timm H, Weigand H, Weiss M, Leese F, Rahmann S. ddRAGE: A data set generator to evaluate ddRADseq analysis software. Mol Ecol Resour. 2018;18:681\u2013690. https://doi.org/10.1111/1755-0998.12743\n\nBibTeX version:\n\n.. code-block:: latex\n\n    @article{timm2018ddrage,\n      title={ddrage: A data set generator to evaluate ddRADseq analysis software},\n      author={Timm, Henning and Weigand, Hannah and Weiss, Martina and Leese, Florian and Rahmann, Sven},\n      journal={Molecular Ecology Resources},\n      volume={18},\n      number={3},\n      pages={681--690},\n      year={2018},\n      url = {http://dx.doi.org/10.1111/1755-0998.12743},\n      doi = {10.1111/1755-0998.12743},\n    }\n\n\n",
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