grenedalf: population genetic statistics for the next generation of pool sequencing

作者：Lucas Czech, Jeffrey P. Spence, Moisés Expósito‐Alonso · 发表于：Bioinformatics · 年份：2024 · DOI：10.1093/bioinformatics/btae508 · 被引用次数：46 · 研究领域：Genetic diversity and population structure、Genomics and Phylogenetic Studies、Genetic Associations and Epidemiology

SUMMARY: Pool sequencing is an efficient method for capturing genome-wide allele frequencies from multiple individuals, with broad applications such as studying adaptation in Evolve-and-Resequence experiments, monitoring of genetic diversity in wild populations, and genotype-to-phenotype mapping. Here, we present grenedalf, a command line tool written in C++ that implements common population genetic statistics such as θ, Tajima's D, and FST for Pool sequencing. It is orders of magnitude faster than current tools, and is focused on providing usability and scalability, while also offering a plethora of input file formats and convenience options. AVAILABILITY AND IMPLEMENTATION: grenedalf is published under the GPL-3, and freely available at github.com/lczech/grenedalf.