Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

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Human Genome Assembly in 100 MinutesPreprint

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Accurate chromosome-scale haplotype-resolved assembly of human genomesPreprint

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Dense and accurate whole-chromosome haplotyping of individual genomesPreprint

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Construction of Whole Genomes from Scaffolds Using Single Cell Strand-Seq Data

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The complete sequence of a human genome

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Long-read human genome sequencing and its applications

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A draft human pangenome reference.

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Haplotype-resolved assembly of diploid genomes without parental data

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HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long readsPreprint

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Telomere-to-telomere assembly of diploid chromosomes with Verkko

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Highly accurate long-read HiFi sequencing data for five complex genomes

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Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

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Nanopore Technology and Its Applications in Gene Sequencing

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Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

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Genome architecture and tetrasomic inheritance of autotetraploid potato

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Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

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Applications of long-read sequencing to Mendelian genetics

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LongPhase: an ultra-fast chromosome-scale phasing algorithm for small and large variants

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Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly

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Genome structural variation in human evolution

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A high-quality bonobo genome refines the analysis of hominid evolution

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Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

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Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data

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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

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Strainberry: automated strain separation in low-complexity metagenomes using long reads

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Gaps and complex structurally variant loci in phased genome assemblies

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A Draft Human Pangenome ReferencePreprint

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The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

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Long-read whole-genome analysis of human single cells

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Merqury: reference-free quality, completeness, and phasing assessment for genome assembliesPreprint

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Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References

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A chromosome‐scale assembly of the bilberry genome identifies a complex locus controlling berry anthocyanin composition

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A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

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A 25-year odyssey of genomic technology advances and structural variant discovery

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An integrated personal and population-based Egyptian genome reference

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State-of-the-art genome inference in the human MHC

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De novo diploid genome assembly using long noisy reads

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Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq

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Fc gamma receptors: Their evolution, genomic architecture, genetic variation, and impact on human disease

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Inversion polymorphism in a complete human genome assembly

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Construction of Strand-seq libraries in open nanoliter arrays

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Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data

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Phase Resolution of Heterozygous Sites in Diploid Genomes is Important to Phylogenomic Analysis under the Multispecies Coalescent Model

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A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk lociPreprint

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A survey of current methods to detect and genotype inversions

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FixItFelix: improving genomic analysis by fixing reference errors

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Probably Correct: Rescuing Repeats with Short and Long Reads

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Advances in the discovery and analyses of human tandem repeats

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Construction and analysis of the chromosome-level haplotype-resolved genomes of two Crassostrea oyster congeners: Crassostrea angulata and Crassostrea gigas

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The role of structural variations in Alzheimer’s disease and other neurodegenerative diseases

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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

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Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data

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Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes

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What a finding of gene copy number variation can add to the diagnosis of developmental neuropsychiatric disorders

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Robust haplotype-resolved assembly of diploid individuals without parental dataPreprint

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Haplotype-resolved Chinese male genome assembly based on high-fidelity sequencing

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Decoding sex: Elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes

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BubbleGun: enumerating bubbles and superbubbles in genome graphs

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Detection of trait-associated structural variations using short-read sequencing

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Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients

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A deep dive into genome assemblies of non-vertebrate animals

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NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data

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Profiling genes encoding the adaptive immune receptor repertoire with gAIRR Suite

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Dominance vs epistasis: the biophysical origins and plasticity of genetic interactions within and between alleles

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Haplotype Shuffling and Dimorphic Transposable Elements in the Human Extended Major Histocompatibility Complex Class II Region

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Generation of lineage-resolved complete metagenome-assembled genomes by precision phasingPreprint

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Highly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution

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A telomere-to-telomere phased genome of an octoploid strawberry reveals a receptor kinase conferring anthracnose resistance

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Identification and Genotyping of Transposable Element Insertions From Genome Sequencing Data

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Telomere-to-Telomere and Haplotype-Phased Genome Assemblies of the Heterozygous Octoploid ‘Florida Brilliance’ Strawberry (Fragaria × ananassa)Preprint

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ASHLEYS: automated quality control for single-cell Strand-seq data

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Locityper enables targeted genotyping of complex polymorphic genes

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MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

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FiMAP: A fast identity-by-descent mapping test for biobank-scale cohorts

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Impact and characterization of serial structural variations across humans and great apes

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Focused Strategies for Defining the Genetic Architecture of Congenital Heart Defects

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New algorithms for accurate and efficient de novo genome assembly from long DNA sequencing reads

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Coverage-preserving sparsification of overlap graphs for long-read assembly

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Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

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Assembly and diploid architecture of an individual human genome via single-molecule technologies

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Graphasing: phasing diploid genome assembly graphs with single-cell strand sequencing

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Chromosome-scale, haplotype-resolved assembly of human genomes

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