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

With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the
computational challenge of efficiently and accurately constructing multiple genome …

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 …

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 …

Background In fungal plant pathogens, genome rearrangements followed by selection
pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and …

Compacted de Bruijn graphs are one of the most fundamental data structures in
computational genomics. Colored compacted de Bruijn graphs are a variant built on a …

Bacterial genomes are simpler than mammalian ones, and yet assembling the former from
the data currently generated by high-throughput short-read sequencing machines still …

Motivation: Genomics is expanding from a single reference per species paradigm into a
more comprehensive pan-genome approach that analyzes multiple individuals together. A …

Despite the rapid development of sequencing technologies, the assembly of mammalian-
scale genomes into complete chromosomes remains one of the most challenging problems …

The de Bruijn graph plays an important role in bioinformatics, especially in the context of de
novo assembly. However, the representation of the de Bruijn graph in memory is a …