INTRODUCTION Modern genomics depends on inexpensive short-read sequencing.
Sequenced reads up to a few hundred base pairs in length are computationally mapped to …

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

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

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, etc. In …

Variation graphs, which represent genetic variation within a population, are replacing
sequences as reference genomes. Path indexes are one of the most important tools for working …

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 …

Here the Human Pangenome Reference Consortium presents a first draft of the human
pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of …

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

We propose a generic approach to replace the canonical sequence representation of
genomes with graph representations, and study several applications of such extensions. We …

A repetitive sequence collection is a set of sequences which are small variations of each other.
A prominent example are genome sequences of individuals of the same or close species, …