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

The human reference genome is part of the foundation of modern human biology and a
monumental scientific achievement. However, because it excludes a great deal of common …

Reference genomes guide our interpretation of DNA sequence data. However, conventional
linear references represent only one version of each locus, ignoring variation in the …

Genome graphs can represent genetic variation and sequence uncertainty. Aligning
sequences to genome graphs is key to many applications, including error correction …

Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

Abstract The famous Burrows–Wheeler Transform (BWT) was originally defined for a single
string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs …

Motivation The variation graph toolkit (VG) represents genetic variation as a graph. Although
each path in the graph is a potential haplotype, most paths are non-biological, unlikely …

There is growing interest in using genetic variants to augment the reference genome into a
graph genome, with alternative sequences, to improve read alignment accuracy and reduce …

Motivation Indexing reference sequences for search—both individual genomes and
collections of genomes—is an important building block for many sequence analysis tasks …

Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field
uses population-level genome reference structures, typically consisting of a sequence …