High-throughput sequencing data sets are usually deposited in public repositories (eg, the
European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached …

Processing large data sets has become an essential part of computational genomics.
Greatly increased availability of sequence data from multiple sources has fueled …

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based
assemblers reduce the complexity by compacting paths into single vertices, but this is …

Motivation A dictionary of k-mers is a data structure that stores a set of n distinct k-mers and
supports membership queries. This data structure is at the hearth of many important tasks in …

Motivation In this work we present REINDEER, a novel computational method that performs
indexing of sequences and records their abundances across a collection of datasets. To the …

The de Bruijn graph is a key data structure in modern computational genomics, and
construction of its compacted variant resides upstream of many genomic analyses. As the …

Given the popularity and elegance of k-mer-based tools, finding a space-efficient way to
represent a set of k-mers is important for improving the scalability of bioinformatics analyses …

The κ-spectrum of a string is the set of all distinct substrings of length κ occurring in the
string. This is a lossy but computationally convenient representation of the information in the …

In this article, we introduce the Conway–Bromage–Lyndon (CBL) structure, a compressed,
dynamic and exact method for representing k-mer sets. Originating from Conway and …

Minimizers are ubiquitously used in data structures and algorithms for efficient searching,
mapping, and indexing of high-throughput DNA sequencing data. Minimizer schemes select …