.. _zonkey_pipeline:

Zonkey Pipeline
===============

**Table of Contents:**

.. toctree::

   overview.rst
   requirements.rst
   configuration.rst
   usage.rst
   panel.rst
   filestructure.rst

The Zonkey Pipeline is a easy-to-use pipeline designed for the analyses of low-coverage, ancient DNA derived from historical equid samples, with the purpose of determining the species of the sample, as well as determining possible hybridization between horses, zebras, and asses (see :ref:`zonkey_usage`). This is accomplished by comparing one or more samples aligned against the *Equus caballus* 2.0 reference sequence with a reference panel of modern equids, including wild and domesticated equids. The reference panel is further described in the :ref:`zonkey_panel` section.

The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite

  Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 2007 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_.

The sequencing data used in the Zonkey publication is available on `ENA`_ under the accession number `PRJEB15037`_.

.. _ENA: https://www.ebi.ac.uk/ena/
.. _PRJEB15037: https://www.ebi.ac.uk/ena/data/view/PRJEB15037
