The table below shows the selected publications. Please refer to NCBI PubMed Collection and bioRxiv channel for the full collection.
Please refer to the complete protocol via HPRC Publication Protocol.
A draft human pangenome reference
Increased mutation rate and gene conversion within human segmental duplications
Recombination between heterologous human acrocentric chromosomes
Pangenome graph construction from genome alignment with minigraph-cactus
Gaps and complex structurally variant loci in phased genome assemblies
AGC: compact representation of assembled genomes with fast queries and updates
Unbiased pangenome graphs
GBZ File Format for Pangenome Graphs
Automated assembly of high-quality diploid human reference genomes
Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
KmerKeys: a web resource for searching indexed genome assemblies and variants
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders
Metagenome assembly of high-fidelity long reads with hifiasm-met
The Human Pangenome Project: a global resource to map genomic diversity.
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.
Segmental duplications and their variation in a complete human genome.
StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps.
The UCSC Genome Browser database: 2022 update.
Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs
Targeted long-read sequencing identifies missing disease-causing variation
lra: A long read aligner for sequences and contigs
The qBED track: a novel genome browser visualization for point processes
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis
A high-quality bonobo genome refines the analysis of hominid evolution
The Need for a Human Pangenome Reference Sequence
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
The structure, function and evolution of a complete human chromosome 8
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
Chromosome-scale, haplotype-resolved assembly of human genomes
A map of cis-regulatory elements and 3D genome structures in zebrafish
The design and construction of reference pangenome graphs with minigraph
Cell-type-specific 3D epigenomes in the developing human cortex
Tissue-specific usage of transposable element-derived promoters in mouse development
Telomere-to-telomere assembly of a complete human X chromosome
Epigenomics and genotype-phenotype association analyses reveal conserved genetic architecture of complex traits in cattle and human
The design and construction of reference pangenome graphs
Genotyping structural variants in pangenome graphs using the vg toolkit
A fully phased accurate assembly of an individual human genome
Progressive alignment with Cactus: a multiple-genome aligner for the thousand-genome era
Efficient de novo assembly of eleven human genomes using PromethION sequencing and a novel nanopore toolkit
We would like to acknowledge the National Genome Research Institute (NHGRI) for funding the following grants supporting the creation of the human pangenome reference: 1U41HG010972, 1U01HG010971, 1U01HG010961, 1U01HG010973, 1U01HG010963, and the Human Pangenome Reference Consortium.