This site includes:
Scripts:
- Script for demultiplexing in
sabre
(Step1_sabre.sh) - Scripts mapping reads against reference genome using
bowtie2
(Step2_Bowtie.sh) - Scripts for creating VCF files in
GATK-HC
(Step3_GATK_preparation.sh and Step4_GATK_vcf.sh) - R scripts for filtering variants, and population genetic analysis (Step5_Data_Processing.Rmd)
Datasets:
- CSV file with all population information for each sample (Rub_frag_list.csv)
- Text file with read information per sample (reads.txt)