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What is assessPool?

Pooling individual samples before sequencing (pool-seq) can greatly reduce cost while producing allele frequencies of single nucleotide polymorphisms (SNPs), but can be difficult to analyze. assessPool is a user-friendly R pipeline designed to analyze population structure from pool-seq data. Our software accepts a variant-call format (VCF) file and a FASTA-formatted reference, providing a straightforward transition from commonly used pipelines such as Stacks or dDocent. AssessPool can handle a variable number of pools and uses Popoolation2 to generate locus-by-locus pairwise FST values and associated Fisher T-test values as measures of population structure, and generates visuals to aid in assessing relationships between pools as well as coverage-based trends.

What does this software do?

• Filters SNPs based on adjustable criteria using vcftools and vcflib
• Determines pool number and prepares proper data structure for analysis
• Creates a customizable run script for Popoolation2 for all pairwise comparisons
• Runs Popoolation2 for each pair of pooled samples
• Generates population genetic statistics and plots for data visualization

For more information, check out the quick start or the manual! Contact us with bugs or questions by submitting an issue via github, or emailing us at [email protected].