k-mer approaches for biodiversity genomics

The wide array of currently available genomes displays a wonderful diversity in size, composition, and structure and is quickly expanding thanks to several global biodiversity genomics initiatives. However, sequencing of genomes, even with the latest technologies, can still be challenging for both technical (e.g., small physical size, contaminated samples, or access to appropriate sequencing platforms) and biological reasons (e.g., germline-restricted DNA, variable ploidy levels, sex chromosomes, or very large genomes). In recent years, k-mer-based techniques have become popular to overcome some of these challenges. They are based on the simple process of dividing the analyzed sequences (e.g., raw reads or genomes) into a set of subsequences of length k, called k-mers, and then analyzing the frequency or sequences of those k-mers. Analyses based on k-mers allow for a rapid and intuitive assessment of complex sequencing data sets. Here, we provide a comprehensive review to the theoretical properties and practical applications of k-mers in biodiversity genomics with a special focus on genome modeling.