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README.md

assessPool v2.0.0

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 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 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!

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Pool-Seq analysis software

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