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ddRAGE - ddRAD Data Generator
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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
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System Requirements
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- python >= 3.5
- numba
- numpy
- matplotlib
- pyyaml
- scipy
For the docs:
- sphinx
For parameter visualization:
- bokeh
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Installation
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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.
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Usage
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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/>`_.
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Citing ddRAGE
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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},
}
