2024/09/08 by Camille Marchet, Marchet, Camille · 2 citations
Physics and Astronomy · Psychology · #Color Science and Applications #Color perception and design #FOS: Biological sciences #Genomics (q-bio.GN)
paper · pdf · doi:10.48550/arxiv.2409.05214
openalex publication_date 2024/09/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.