Adam Park

Sep 15, 2024 | biorxiv.org | Adam Park |David Koslicki

AbstractDespite the widespread adoption of k-mer-based methods in bioinformatics, understanding the influence of k-mer sizes remains a persistent challenge. Selecting an optimal k-mer size or employing multiple k-mer sizes is often arbitrary, application-specific, and fraught with computational complexities. Typically, the influence of k-mer size is obscured by the outputs of complex bioinformatics tasks, such as genome analysis, comparison, assembly, alignment, and error correction.

Jun 1, 2024 | biorxiv.org | Adam Park |David Koslicki

AbstractDespite the widespread adoption of k-mer-based methods in bioinformatics, a fundamental question persists: How can we quantify the influence of k sizes in applications? With no universal answer available, choosing an optimal k size or employing multiple k sizes remains application-specific, arbitrary, and computationally expensive.

Jan 28, 2024 | biorxiv.org | Adam Park |David Koslicki

AbstractDespite the widespread adoption of k-mer-based methods in bioinformatics, a fundamental question persists: How to elucidate the structural transition of a k-mer set when the order switches to k'? Lacking a generalized answer, the problem has been considered application-specific, necessitating the effect of k to be studied empirically in each k-mer-based method, e.g. in areas of genome complexity, assembly, error corrections, etc.

Nov 23, 2023 | biorxiv.org | Adam Park |David Koslicki

AbstractDespite the widespread adoption of k-mer-based methods in bioinformatics, a fundamental question persists: How to elucidate the structural transition of a k-mer set when the order switches to k'? Attaining a generalized answer has significant implications to k-mer-based methods where the influence of k has been empirically analyzed (eg. in areas of assembly, genome comparison, etc.).

Nov 21, 2023 | biorxiv.org | Adam Park |David Koslicki

AbstractDespite the widespread adoption of k-mer-based methods in bioinformatics, a fundamental question persists: How to elucidate the structural transition of a k-mer set when the order switches to k'? Attaining a generalized answer has significant implications to k-mer-based methods where the influence of k have been empirically analyzed (eg. in areas of assembly, genome comparison, etc.).