assessPool v2 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.

Quick Start

1. 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

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 {renv}) 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 '

   Example data can be accessed via Zenodo

See the wiki for more information!