Chromosomal-level genome assembly of the scimitar-horned oryx: insights into diversity and demography of a species extinct in the wild
Emily Humble, Pavel Dobrynin, Helen Senn, Justin Chuven, Alan F Scott, David W Mohr, Olga Dudchenko, Arina D Omer, Zane Colaric, Erez Lieberman Aiden, David Wildt, Shireen Oliaji, Gail Tamazian, Budhan Pukazhenthi, Rob Ogden, Klaus-Peter Koepfli
Manuscript available here
This repository contains the scripts used for downstream analyses and visualisation including synteny plotting, genetic diversity analyses, PSMC simulations and PSMC visualisation. Please see github repository SHO_reseq_2020 for prior steps including alignment and SNP calling.
Most intermediate data files required to run these scripts are available on the Dryad Digital Repository. Otherwise, files can be generated using scripts from the first part of the pipeline.
/scripts contains a few extra scripts that are required for analyses.