Prokrustean Graph: A substring index for rapid k-mer size analysis.

ABSTRACT: The widespread adoption of k-mers in bioinformatics has led to efficient methods utilizing genomic sequences in a variety of biological tasks. However, understanding the influence of k-mer sizes within these methods remains a persistent challenge, as the outputs of complex bioinformatics pipelines obscure this influence with various noisy factors. The choice of k-mer size is often arbitrary, with justification frequently omitted in the literature and method tutorials. Furthermore, recent methods employing multiple k-mer sizes encounter significant computational challenges. Nevertheless, most methods are built on well-defined objects related to k-mers, such as de Bruijn graphs, Jaccard similarity, Bray-Curtis dissimilarity, and k-mer spectra. The ro

SUBMITTER: Park A 

PROVIDER: S-EPMC11160577 | biostudies-literature | 2025 Jun

REPOSITORIES: biostudies-literature