https://github.com/dereneaton/ipyrad

Interactive assembly and analysis of RAD-seq data sets
https://github.com/dereneaton/ipyrad

assembly genomics phylogeny rad-seq

Last synced: about 4 hours ago
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Interactive assembly and analysis of RAD-seq data sets

• Host: GitHub
• URL: https://github.com/dereneaton/ipyrad
• Owner: dereneaton
• License: gpl-3.0
• Created: 2015-10-07T16:50:52.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2025-01-07T22:12:20.000Z (25 days ago)
• Last Synced: 2025-01-26T01:09:33.763Z (7 days ago)
• Topics: assembly, genomics, phylogeny, rad-seq
• Language: Jupyter Notebook
• Homepage: http://ipyrad.readthedocs.io
• Size: 98.8 MB
• Stars: 73
• Watchers: 7
• Forks: 41
• Open Issues: 60
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt
  • Support: docs/support.rst

Awesome Lists containing this project

README

        
*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 (``_),

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 `_.

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 `_  

+ `Isaac Overcast `_