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 …

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 …

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

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

… If we take d(i,j) to be |i−j|, then it can be shown that LPC 0 is equivalent to the complement of
… Alternatively, we can take d(i,j) to be the genomic distance between the variants, measured …

… Let x i be a k-mer in the reference sequence S, and let e j be an event in the event
sequence E and e j ⋄x i mean that event e j is aligned to k-mer x i . The model calculates P(e …

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

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

There has been tremendous progress in phased genome assembly production by combining
long-read data with parental information or linked-read data. Nevertheless, a typical …