Stacks

Stacks processes and analyzes massively parallel short-read sequencing data (e.g., RADseq and GBS, including restriction enzyme–based sequence data) to compute population-genomic summary statistics and perform SNP-level and sliding-window analyses for population genomics and phylogeography.

Key Features:

• Data Processing and Analysis: Processes restriction enzyme‑based RADseq and genotype-by-sequencing (GBS) short-read datasets and scales to tens of thousands of genetic markers.
• Population Genomic Summary Statistics: Generates core statistics including allele frequencies, heterozygosity, and linkage disequilibrium.
• SNP-by-SNP Statistical Tests: Performs statistical tests at individual SNPs to identify significant genetic variation across populations.
• Sliding Window Analysis: Calculates statistics across a reference genome using a smoothed sliding-window approach to identify genomic regions of interest.
• Flexible Output Formats: Exports results in multiple output formats compatible with downstream analysis packages.

Scientific Applications:

• Genetic Mapping: Supports construction of genetic maps to elucidate relationships among genetic markers.
• Population Genomics: Enables studies of genetic variation, structure, and summary statistics within and between populations.
• Phylogeography: Facilitates analysis of geographic distribution of genetic lineages using RADseq/GBS data.

Methodology:

Processes massively parallel short-read RADseq and GBS data, computes allele frequencies, heterozygosity and linkage disequilibrium, performs SNP-by-SNP statistical tests, conducts smoothed sliding-window analyses across a reference genome, and exports results in multiple formats.