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

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>_