The amount of biological sequencing data available in public repositories is growing
exponentially, forming an invaluable biomedical research resource. Yet, making all this …

High‐throughput sequencing has become an increasingly central component of microbiome
research. The development of de Bruijn graph‐based methods for assembling high …

Abstract Motivation: The de Bruijn graph has become a ubiquitous graph model for
biological data ever since its initial introduction in the late 1990s. It has been used for a …

The recent growth of microbial sequence data allows comparisons at unprecedented scales,
enabling the tracking of strains, mobile genetic elements, or genes. Querying a genome …

This paper provides a comprehensive survey of data structures for representing k-mer sets,
which are fundamental in high-throughput sequencing analysis. It categorizes the methods …

Technological advances made over the last decades in sequencing technologies have led
to continuous improvements of quality and ever-decreasing costs of sequencing. All this …

Given a string S over an alphabet of size σ, we consider practical implementations of
extended compressed RAM on S, which supports access, replace, lnsert, and delete …

Ever-decreasing genome sequencing costs have led to an explosion in sequencing
throughput, with the global sequencing capacity expected to exceed one exabyte per year in …

Abstract (EN) Much of our understanding of eukaryotic life has come from studying
mitochondrial DNA, giving rise to leading hypotheses in evolution. To enable these studies …

Colored de Bruijn graphs, extensions of the de Bruijn graphs are fundamental data
structures for the analysis of high-throughput sequencing data. Although colored de Bruin …