*ipyrad*: interactive assembly and analysis of RAD-seq data sets
--------------------------------------------------------------

Welcome to ipyrad, an interactive toolkit for assembly and analysis of 
restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) 
for population genetic and phylogenetic studies.

Documentation
---------
Full documentation is available here (`<http://ipyrad.readthedocs.io>`_),
where you will find installation instructions, example tutorials, and a full user guide.


Quick Install
------------
ipyrad is available through the Python package installer `conda` with all dependencies included.
If you have `conda` installed you can simply run:

    conda install ipyrad -c conda-forge -c bioconda


If you do not have `conda` installed then you will enjoy our 
`complete installation instructions <https://ipyrad.readthedocs.io/en/master/3-installation.html>`_.

Run ipyrad in Binder
--------------------
.. image:: https://mybinder.org/badge_logo.svg
    :alt: Launch ipyrad in a binder instance
    :target: https://mybinder.org/v2/gh/dereneaton/ipyrad/master

Getting Help
------------
Join the ipyrad gitter channel and ask a question, request a feature, or flame the developers:

.. image:: https://badges.gitter.im/Join%20Chat.svg
   :alt: Join the chat at https://gitter.im/dereneaton/ipyrad
   :target: https://gitter.im/dereneaton/ipyrad?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge


License
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GPLv3

Cite the Manuscript
-------------------
Eaton DAR & Overcast I. "ipyrad: Interactive assembly and analysis of RADseq datasets." Bioinformatics (2020).

Contributors
------------
+ `Deren Eaton <deren.eaton@yale.edu>`_  
+ `Isaac Overcast <isaac.overcast@gmail.com>`_