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
Summary
This repository contains the scripts used for aligning reads and calling SNPs for resequenced individuals, assembling mitogenomes, running ANGSD, running MaCS and running PSMC.
For subsequent analyses described in the paper, please see github repository SHO_analysis_2020.
Data
Sequencing reads required to run the pipeline are available at the European Nucleotide Archive (https://www.ebi.ac.uk/ena/browser) under study accession PRJEB37295.
Genome assembly used in the pipeline is available on the DNA ZOO website. For the steps run here, only the 29 chromosomal-level scaffolds were used.
Notes
4.2_boot_PSMC.sh, 6.1_angsdHet.sh and 6.1_realSFS.sh are designed to be run using the respective scripts run_4.2_boot_PSMC.sh, run_6.1_angsdHet.sh and run_6.1_realSFS.sh.
/file_lists contains text files required for running the pipeline.