Population genomics of Acropora kenti on the Great Barrier Reef

This repository contains computational methods including source code and explanatory notes for paper published in:

Jia Zhang, Nadja M. Schneller, Matt A. Field, Cheong Xin Chan, David J. Miller, Jan M. Strugnell, Cynthia Riginos, Line Bay, Ira Cooke. Molecular Ecology. https://doi.org/10.1111/mec.17468

This repository has also been archiinved on Zenodo:

Analysis and code included in this project:

Sequencing data processing

• Sampling information and data sequencing
• Read alignment
• Quality control of sites and samples

Population structure, batch effects and variant calling

• Genotype Likelihoods
• Population Structure
• Batch effects

Symbionts

• Symbiont profiles and symbiont haplogroups

Inversions

• Finding Inversions using PCAngsd
• Genotyping Inversions
• Individual heterozygosity
• Linkage disequilibrium around inversions
• Genetic Distances between inversion haplotypes
• Variant Severity
• Test for spatial and ecological association