Year: 2021
Type: article
Abstract: The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k -mers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying a k -mer set has emerged as a shared underlying component. A set of k -mers has unique features and applications that, over the past 10 years, have resulted in many specialized approaches for its representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query a k -mer set. We hope this survey will serve as a resource for researchers in the field as well as make the area more accessible to researchers outside the field.
Source: ACM Computing Surveys
DOI: 10.1145/3445967
Authors: Rayan Chikhi, Jan Holub, Paul Medvedev
Institution: Czech Technical University in Prague
Language: English
Subfield: Artificial Intelligence
Field: Computer Science
Domain: Physical Sciences
Open Access status: hybrid
Awards: Y Chromosome Evolution, Cryptic Speciation in Acanthocyclops Vernalis Complex (Crustacea: Copepoda): the Hypothesized Role of Chromatin Diminution, G1935710221, ABI Innovation: A Novel Framework for Detecting Genomic Structural Variation, III: Small: Reconstructing viral population without using a reference genome, CAREER: De Novo Assembly of Large Genomic Data, G4431402795, Institut Convergences pour l’étude de l’Emergence des Pathologies au Travers des Individus et des populatiONs, G5420063140, G5641063287, G6761430300, G718049477, G8744824220
OpenAlex ID: W3134677442