Metadata-Version: 2.1
Name: ddrage
Version: 1.5.1
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: #############################
        ddRAGE - ddRAD Data Generator
        #############################
        
        
        ddRAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads.
        The generated data sets 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
        
        For parameter visualization:
        
        - bokeh
        
        
        ************
        Installation
        ************
        
        We recommend the installation using conda:
        
        .. code-block:: shell
        
           $ conda create -n ddrage -c bioconda ddrage
           $ source activate ddrage
        
        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 ddrage
           $ cd ddrage
           /rage$ python setup.py install
        
        In this case you have to install the requirements listed above.
        
        
        *****
        Usage
        *****
        
        To simulate a ddRAD data set, call ddrage from the command line:
        
        .. code-block:: shell
        
           $ ddrage
        
        you can specify parameters to change data set parameters such as number of individuals (``-n``), nr of loci (``-l``), and coverage (``--coverage``):
        
        .. code-block:: shell
        
           $ ddrage -n 6 -l 10000 --coverage 30
        
        This creates a data set with reads from 6 individuals at 10000 loci with an expected coverage of 30.
        
        A more detailed tutorial can be found `on readthedocs <https://ddrage.readthedocs.io/en/latest/getting-started/>`_.
        
        
        *************
        Citing ddRAGE
        *************
        
        Our paper describing ddRAGE has been published in `Molecular Ecology Resources <http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12743/full>`_.
        You can cite it as follows:
        
        .. code-block:: text
                        
            Timm H, Weigand H, Weiss M, Leese F, Rahmann S. ddRAGE: A data set generator to evaluate ddRADseq analysis software. Mol Ecol Resour. 2017;00:1–10. https://doi.org/10.1111/1755-0998.12743
        
        BibTeX version:
        
        .. code-block:: latex
        
            @article {timm2017ddrage,
              author = {Timm, Henning and Weigand, Hannah and Weiss, Martina and Leese, Florian and Rahmann, Sven},
              title = {ddRAGE: A data set generator to evaluate ddRADseq analysis software},
              journal = {Molecular Ecology Resources},
              year={2017},
              issn = {1755-0998},
              pages = {n/a--n/a},
              url = {http://dx.doi.org/10.1111/1755-0998.12743},
              doi = {10.1111/1755-0998.12743},
            }
        
        Note that, since the final version of the issue has not been published in print yet, the page numbers are still missing.
        We will add them once they are available.
        
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: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Provides-Extra: BBD-visualization
Provides-Extra: documentation
