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 …

Long-read sequencing has the potential to transform variant detection by reaching currently
difficult-to-map regions and routinely linking together adjacent variations to enable read-…

DNA chemical modifications regulate genomic function. We present a framework for mapping
cytosine and adenosine methylation with the Oxford Nanopore Technologies MinION …

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 …

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 …

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

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 …