Mobile genetic elements are key to the evolution of bacteria and traits that affect host and
ecosystem health. Here, we use a framework of a hierarchical and modular system that …

Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

Pangenome graphs can represent all variation between multiple reference genomes, but
current approaches to build them exclude complex sequences or are based upon a single …

The recent advances in sequencing technologies enable the assembly of individual
genomes to the quality of the reference genome. How to integrate multiple genomes from …

Although most existing genome assemblers are based on de Bruijn graphs, the construction
of these graphs for large genomes and large k-mer sizes has remained elusive. This …

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 Pangenome variation graphs model the mutual alignment of collections of DNA
sequences. A set of pairwise alignments implies a variation graph, but there are no scalable …

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

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 …

Background As a single reference genome cannot possibly represent all the variation
present across human individuals, pangenome graphs have been introduced to incorporate …