Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

The rapid development of high-throughput sequencing technologies means that hundreds of
gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools …

The assembly of DNA sequences de novo is fundamental to genomics research. It is the first
of many steps toward elucidating and characterizing whole genomes. Downstream …

Counting all k-mers in a given dataset is a standard procedure in many bioinformatics
applications. We introduce KMC3, a significant improvement of the former KMC2 algorithm …

Motivation: Genome assembly tools based on the de Bruijn graph framework rely on a
parameter k, which represents a trade-off between several competing effects that are difficult …

The recent breakthroughs in assembling long error-prone reads were based on the overlap-
layout-consensus (OLC) approach and did not utilize the strengths of the alternative de …

The emergence of drug-resistant tuberculosis is a major global public health concern that
threatens the ability to control the disease. Whole-genome sequencing as a tool to rapidly …

Bacteria pose unique challenges for genome-wide association studies because of strong
structuring into distinct strains and substantial linkage disequilibrium across the genome 1 …

Abstract Background The de Bruijn graph data structure is widely used in next-generation
sequencing (NGS). Many programs, eg de novo assemblers, rely on in-memory …

Motivation: Building the histogram of occurrences of every k-symbol long substring of
nucleotide data is a standard step in many bioinformatics applications, known under the …