Pool-Seq analysis software
- Filters SNPs based on adjustable criterion with suggestions for pooled data
- Determines pool number and prepares proper data structure for analysis
- Creates a customizable run script for Popoolation2 for all pairwise comparisons
- Runs Popoolation2 and poolfstat
- Imports Popoolation2 and poolfstat output
- Generates population genetic statistics and plots for data visualization.
- To run assessPool, you will need: R v3.6.0 or higher, RStudio, samtools, CPAN, vcftools v0.1.12 or higher, vcflib, and (optionally) GNU parallel
- Navigate to desired working directory on your computer
- Clone repo into directory:
git clone https://github.com/ToBoDev/assessPool.git
- Open assessPool Rproject in RStudio
- Open assessPool_main.Rmd file in RStudio
- Make sure you have your SNP file (.vcf) and reference file (.fasta) in the working directory
- Note - the first time you run the script, library installation (via packrat) will take some time.
- Follow the steps in the main file to complete your analysis - run each code chunk and adjust parameters as needed
See the wiki for more information!