README.md

Genetics of Acropora tenuis on the GBR using shallow whole genome resequencing

Shell scripts and R code to accompany the paper

Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

Raw Data Processing

• Read Alignment and Preprocessing
• Summary of Read Mapping Rates
• Variant calling
• Variant filtering
• Host mitochondrial genome assembly
• Host mitochondrial haplotype network
• Symbiont mitochondrial haplotype network
• Scans for Fst outliers

Downstream Analysis and Plots

• Population Structure : Rmd file 01_population_structure.Rmd
• Estimating Mutation Rate : Rmd file 02_mutation_rates.Rmd
• Demographic History with MSMC : Rmd file 03_msmc.Rmd
• Demographic History with dadi : Rmd file 04_dadi.Rmd
• Selective Sweep Detection with SweepFinder 2 : Rmd file 05_sf2_thresholds.Rmd
• Interpretation of SweepFinder results : Rmd file 06_sf2.Rmd
• Preparation of data for Bayescan : Rmd file 17_thin_afs.Rmd
• Fst outlier detection with Bayescan 2 : Rmd file 19_bayescan.Rmd
• Neutrality and Diversity statistics with ANGSD : Rmd file 07_popgen_stats.Rmd
• Symbiont Profiles with kraken : Rmd file (08_metagenome.Rmd)
• Analysis of interspersed repeats : Rmd file (09_repeats.Rmd)
• Statistical Analysis of Symbiont Haplotypes : Rmd file 10_haplonetworks.Rmd
• Summary of Read Mapping Rates : Rmd file 13_mapping.Rmd
• Outlier analysis with Bayescan : Rmd file 19_bayescan.Rmd

All of the sections above are provided as processed markdown files. Clicking the link should display a web readable page with text, a few select commands and plots and tables. The code used to generate these pages is provided in the corresponding .Rmd file. If you would like to run the code in these files yourself you will need to;

1. Checkout this repository

git clone https://github.com/iracooke/atenuis_wgs_pub.git

2. Download additional data not hosted on github due to size constraints

cd atenuis_wgs_pub
wget http://data.qld.edu.au/public/Q5999/iracooke/atenuis_wgs_pub/data.tgz -O data.tgz
tar -zxvf data.tgz 

3. Open the project file atenuis_wgs_pub.Rproj in RStudio and open the desired file (eg 01_population_structure.Rmd). After installing any required R packages the code should run and produce plots and tables identical to those shown in the web links above.