K-mer-based Approaches to Bridging Pangenomics and Population Genetics.

ABSTRACT: Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes can be challenging for many species, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a very useful but underutilized tool for bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patt

SUBMITTER: Roberts MD 

PROVIDER: S-EPMC11925024 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature