Metadata-Version: 2.1
Name: ddrage
Version: 1.7.1
Summary: Simulator for ddRADseq (double digest restriction site associated DNA sequencing) 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. 2018;18:681–690. https://doi.org/10.1111/1755-0998.12743
        
        BibTeX version:
        
        .. code-block:: latex
        
            @article{timm2018ddrage,
              title={ddrage: A data set generator to evaluate ddRADseq analysis software},
              author={Timm, Henning and Weigand, Hannah and Weiss, Martina and Leese, Florian and Rahmann, Sven},
              journal={Molecular Ecology Resources},
              volume={18},
              number={3},
              pages={681--690},
              year={2018},
              url = {http://dx.doi.org/10.1111/1755-0998.12743},
              doi = {10.1111/1755-0998.12743},
            }
        
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: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Provides-Extra: BBD-visualization
Provides-Extra: documentation
