Guide to k-mer approaches for genomics across the tree of life

Abstract

The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing of genomes, even with all the recent advances, 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 analysed sequences (e.g. raw reads or genomes) into a set of sub-sequences of length k, called k-mers. Despite this apparent simplicity, k-mer-based analysis allows for a rapid and intuitive assessment of complex sequencing datasets. Here, we provide the first comprehensive review to the theoretical properties and practical applications of k-mers in biodiversity genomics, serving as a reference manual for this powerful approach.