Stacks: an analysis tool set for population genomics

TLDR

Massively parallel short‑read sequencing and powerful software now enable analysis of tens of thousands of genetic markers, but the rapidly expanding data volumes pose significant processing challenges. The study extends the Stacks software to efficiently analyze genotype‑by‑sequencing data for population studies. The extended Stacks pipeline generates core population genomic statistics, applies smoothed sliding‑window analysis across a reference genome, and outputs data in formats compatible with common downstream tools. Stacks now delivers core population genomic summary statistics, SNP‑by‑SNP tests, and is positioned to harness massively parallel genotyping data for ecological and evolutionary genetics.

Abstract

Abstract Massively parallel short‐read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the S tacks software package to efficiently use genotype‐by‐sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP ‐by‐ SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in S tacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.