This repository contains three pipelines with code and tutorials for analyzing whole-genome sequencing data from the California Conservation Genomics Project (CCGP) for the red abalone species. The code is split into three sections:
- VCF filtering and identification and removal of the putative sex-determining region: https://htmlpreview.github.io/?https://github.com/JoannaGriffiths/CCGP_Red_Abalone/blob/main/Filtering_SDR/Filtering_VCF_and_SDR.html
- Population structure and population genetic analyses: https://htmlpreview.github.io/?https://github.com/JoannaGriffiths/CCGP_Red_Abalone/blob/main/Population_Structure/Population_Structure.html
- Outlier analyses, genome-environment associations, and gene ontology characterization and enrichment: https://htmlpreview.github.io/?https://github.com/JoannaGriffiths/CCGP_Red_Abalone/blob/main/Outlier_Analyses/Outlier_Analyses_Pipeline.html