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Data Structures to Represent a Set of k-long DNA Sequences

Updated: Nov 22, 2022

ACM Computing Surveys

Chikhi R, Holub J, Medvedev P 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.

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