Advances in colored k-mer sets: essentials for the curious
Abstract
This paper provides a comprehensive review of recent advancements in k-mer-based data structures representing collections of several samples (sometimes called colored de Bruijn graphs) and their applications in large-scale sequence indexing and pangenomics. The review explores the evolution of k-mer set representations, highlighting the trade-offs between exact and inexact methods, as well as the integration of compression strategies and modular implementations. I discuss the impact of these structures on practical applications and describe recent utilization of these methods for analysis. By surveying the state-of-the-art techniques and identifying emerging trends, this work aims to guide researchers in selecting and developing methods for large scale and reference-free genomic data. For a broader overview of k-mer set representations and foundational data structures, see the accompanying article on practical k-mer sets.
Keywords
Cite
@article{arxiv.2409.05214,
title = {Advances in colored k-mer sets: essentials for the curious},
author = {Camille Marchet},
journal= {arXiv preprint arXiv:2409.05214},
year = {2024}
}