Quick Start - ToBoDev/assessPool GitHub Wiki

assessPool Quick Start

1. To run assessPool, you will need: Rstudio, samtools, cpan, vcftools v0.1.12 or higher, vcflib, and (optionally) GNU parallel
2. Navigate to desired working directory on your computer
3. Clone repo into directory: git clone https://github.com/ToBoDev/assessPool.git
4. Open assessPool Rproject in RStudio
5. Open assessPool_main.Rmd file in RStudio
6. Make sure you have your SNP file (.vcf) and reference file (.fasta) in the working directory
7. Note - the first time you run the script, library installation (via packrat) will take some time.
8. Follow the steps in the main file to complete your analysis - run each code chunk and adjust parameters as needed