This is best viewed using the github pages site
This is the repository for all code used in the analysis of the GBS dataset used in the comparison between rabbits from the 1996 (n = 59) and 2012 (n = 53) populations from the Gum Creek / Oraparrina region of South Australia.
In addition, some samples from a previous analysis of the Turretfield rabbit population, sampled in 2010 were included as an outgroup.
All bash scripts are available in the folder scripts with four main process being undertaken: 1) Demultiplexing; 2) Read Trimming; 3) Read Alignment, and 4) Running the Stacks Pipeline
The bulk of the data analysis was performed in R with code available in the following locations:
- Checking the results of Demultiplexing
- Checking the quality of alignments
- Filtering of SNPs
- Analysis of filtered SNPs
- Assessment of linkage
- Simulation of Genetic Drift
In addition, a supplementary analysis was performed using the FLK algorithm, however these results were not included in the submitted paper.