Pool-Seq analysis software
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
docs
packrat
scripts
LICENSE
README.md
_config.yml
assessPool.Rproj
assessPool_main.Rmd

README.md

assessPool v1.0.0

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
  • Imports Popoolation2 output
  • Generates population genetic statistics and plots for data visualization.

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

See the wiki for more information!