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 kmers, which are short fixed-length strings present in a dataset. While these approaches are rather diverse, storing and querying k-mer sets has emerged as a shared underlying component. Sets of k-mers have unique features and applications that, over the last ten years, have resulted in many specialized approaches for their representation. In this survey, we give a unified presentation and comparison of the data structures that have been proposed to store and query k-mer sets. We hope this survey will not only serve as a resource for researchers in the field but also make the area more accessible to outsiders.
Membership data structures for k-mer sets were surveyed in a recent paper REF .
Data structures to represent sets of k-long DNA sequences
ArXiv
ArXiv
Computer Science Mathematics Biology