Zonkey Pipeline

Table of Contents:

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 Pipeline 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 Reference 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.

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