ddrage 1.2.0

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/