Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …

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

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

Pangenome references address biases of reference genomes by storing a representative
set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles …

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 …

Motivation Pangenome graphs provide a complete representation of the mutual alignment of
collections of genomes. These models offer the opportunity to study the entire genomic …

Structural variants (SVs) remain challenging to represent and study relative to point
mutations despite their demonstrated importance. We show that variation graphs, as …

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

High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid
genomes, and metagenomes provide important insights into genetic variation associated …

Pangenomes reduce reference bias by representing genetic diversity better than a single
reference sequence. Yet when comparing a sample to a pangenome, variants in the …