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Human Genome Assembly in 100 Minutes

https://doi.org/10.1101/705616
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/11557067openalex-snapshot
Algorithms in Bioinformatics
inferredcites →https://doi.org/10.1007/978-3-662-44753-6_5openalex-snapshot
Efficient Local Alignment Discovery amongst Noisy Long Reads
inferredcites →https://doi.org/10.1007/bf01188580openalex-snapshot
Combinatorial algorithms for DNA sequence assembly
inferredcites →https://doi.org/10.1007/bf01840446openalex-snapshot
AnO(ND) difference algorithm and its variations
inferredcites →https://doi.org/10.1016/j.ajhg.2017.06.005openalex-snapshot
10 Years of GWAS Discovery: Biology, Function, and Translation
inferredcites →https://doi.org/10.1038/nature09792openalex-snapshot
Initial impact of the sequencing of the human genome
inferredcites →https://doi.org/10.1038/nature13907openalex-snapshot
Resolving the complexity of the human genome using single-molecule sequencing
inferredcites →https://doi.org/10.1038/nature20098openalex-snapshot
De novo assembly and phasing of a Korean human genome
inferredcites →https://doi.org/10.1038/nbt.3238openalex-snapshot
Assembling large genomes with single-molecule sequencing and locality-sensitive hashing
inferredcites →https://doi.org/10.1038/nbt.4060openalex-snapshot
Nanopore sequencing and assembly of a human genome with ultra-long reads
inferredcites →https://doi.org/10.1038/nbt.4277openalex-snapshot
De novo assembly of haplotype-resolved genomes with trio binning
inferredcites →https://doi.org/10.1038/nmeth.2474openalex-snapshot
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
inferredcites →https://doi.org/10.1038/nmeth.4035openalex-snapshot
Phased diploid genome assembly with single-molecule real-time sequencing
inferredcites →https://doi.org/10.1038/nrg3933openalex-snapshot
Genetic variation and the de novo assembly of human genomes
inferredcites →https://doi.org/10.1038/s41587-019-0072-8openalex-snapshot
Assembly of long, error-prone reads using repeat graphs
inferredcites →https://doi.org/10.1038/s41587-019-0217-9openalex-snapshot
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
inferredcites →https://doi.org/10.1038/s41592-019-0669-3openalex-snapshot
Fast and accurate long-read assembly with wtdbg2
inferredcites →https://doi.org/10.1093/bioinformatics/btq126openalex-snapshot
PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene–disease associations
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/nar/gkt1229openalex-snapshot
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
inferredcites →https://doi.org/10.1101/gr.213611.116openalex-snapshot
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
inferredcites →https://doi.org/10.1109/tit.2013.2270273openalex-snapshot
Information Theory of DNA Shotgun Sequencing
inferredcites →https://doi.org/10.1111/ahg.12364openalex-snapshot
Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads
inferredcites →https://doi.org/10.1126/science.aae0344openalex-snapshot
Long-read sequence assembly of the gorilla genome
inferredcites →https://doi.org/10.1186/gm483openalex-snapshot
The human genome project: big science transforms biology and medicine
inferredcites →https://doi.org/10.3390/genes9100486openalex-snapshot
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Comparative Evolutionary Genomics in Insects
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Artificial Intelligence and Machine Learning in Clinical Research and Patient Remediation
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Structural variant identification and characterization
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State-of-the-art genome inference in the human MHC
inferred← citeshttps://doi.org/10.1016/j.cels.2021.08.009openalex-snapshot
Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer
inferred← citeshttps://doi.org/10.1016/j.cels.2021.09.010openalex-snapshot
Democratizing long-read genome assembly
inferred← citeshttps://doi.org/10.1016/j.crmeth.2024.100754openalex-snapshot
Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing
inferred← citeshttps://doi.org/10.1016/j.csbj.2019.11.002openalex-snapshot
Long walk to genomics: History and current approaches to genome sequencing and assembly
inferred← citeshttps://doi.org/10.1016/j.heliyon.2024.e38687openalex-snapshot
High-quality chromosome-level genome assembly of female Artemia franciscana reveals sex chromosome and Hox gene organization
inferred← citeshttps://doi.org/10.1016/j.pbi.2019.12.009openalex-snapshot
Building near-complete plant genomes
inferred← citeshttps://doi.org/10.1016/j.xplc.2024.101000openalex-snapshot
Haplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits
inferred← citeshttps://doi.org/10.1016/j.yamp.2022.07.004openalex-snapshot
Applications of Long-Read Sequencing Technology in Clinical Genomics
inferred← citeshttps://doi.org/10.1038/s41467-020-16037-7openalex-snapshot
Effect of sequence depth and length in long-read assembly of the maize inbred NC358
inferred← citeshttps://doi.org/10.1038/s41467-020-18564-9openalex-snapshot
A diploid assembly-based benchmark for variants in the major histocompatibility complex
inferred← citeshttps://doi.org/10.1038/s41467-020-20536-yopenalex-snapshot
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
inferred← citeshttps://doi.org/10.1038/s41467-022-30680-2openalex-snapshot
Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies
inferred← citeshttps://doi.org/10.1038/s41576-020-0236-xopenalex-snapshot
Long-read human genome sequencing and its applications
inferred← citeshttps://doi.org/10.1038/s41576-021-00367-3openalex-snapshot
Towards population-scale long-read sequencing
inferred← citeshttps://doi.org/10.1038/s41576-023-00590-0openalex-snapshot
Variant calling and benchmarking in an era of complete human genome sequences
inferred← citeshttps://doi.org/10.1038/s41576-024-00718-wopenalex-snapshot
Genome assembly in the telomere-to-telomere era
inferred← citeshttps://doi.org/10.1038/s41586-022-05325-5openalex-snapshot
Semi-automated assembly of high-quality diploid human reference genomes
inferred← citeshttps://doi.org/10.1038/s41587-020-00747-wopenalex-snapshot
Efficient hybrid de novo assembly of human genomes with WENGAN
inferred← citeshttps://doi.org/10.1038/s41587-020-0711-0openalex-snapshot
Chromosome-scale, haplotype-resolved assembly of human genomes
inferred← citeshttps://doi.org/10.1038/s41587-020-0719-5openalex-snapshot
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads
inferred← citeshttps://doi.org/10.1038/s41587-021-01108-xopenalex-snapshot
Nanopore sequencing technology, bioinformatics and applications
inferred← citeshttps://doi.org/10.1038/s41587-021-01130-zopenalex-snapshot
Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities
inferred← citeshttps://doi.org/10.1038/s41587-022-01261-xopenalex-snapshot
Haplotype-resolved assembly of diploid genomes without parental data
inferred← citeshttps://doi.org/10.1038/s41587-023-01662-6openalex-snapshot
Telomere-to-telomere assembly of diploid chromosomes with Verkko
inferred← citeshttps://doi.org/10.1038/s41588-022-01043-wopenalex-snapshot
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes
inferred← citeshttps://doi.org/10.1038/s41592-020-01056-5openalex-snapshot
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
inferred← citeshttps://doi.org/10.1038/s41592-023-01914-yopenalex-snapshot
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes
inferred← citeshttps://doi.org/10.1038/s41592-023-02141-1openalex-snapshot
Constructing telomere-to-telomere diploid genome by polishing haploid nanopore-based assembly
inferred← citeshttps://doi.org/10.1038/s41597-023-02251-7openalex-snapshot
PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793
inferred← citeshttps://doi.org/10.1038/s41597-025-04434-wopenalex-snapshot
High-fidelity annotated triploid genome of the quarantine root-knot nematode, Meloidogyne enterolobii
inferred← citeshttps://doi.org/10.1038/s43588-021-00073-4openalex-snapshot
Time- and memory-efficient genome assembly with Raven
inferred← citeshttps://doi.org/10.1073/pnas.2313440121openalex-snapshot
The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom
inferred← citeshttps://doi.org/10.1093/bib/bbac305openalex-snapshot
Complex genome assembly based on long-read sequencing
inferred← citeshttps://doi.org/10.1093/bib/bbag405openalex-snapshot
VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa435openalex-snapshot
Weighted minimizer sampling improves long read mapping
inferred← citeshttps://doi.org/10.1093/bioinformatics/btac244openalex-snapshot
The minimizer Jaccard estimator is biased and inconsistent
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae187openalex-snapshot
Designing efficient randstrobes for sequence similarity analyses
inferred← citeshttps://doi.org/10.1093/bioinformatics/btae493openalex-snapshot
ModDotPlot—rapid and interactive visualization of tandem repeats
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf418openalex-snapshot
Efficient seeding for error-prone sequences with SubseqHash2
inferred← citeshttps://doi.org/10.1093/gbe/evac122openalex-snapshot
A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
inferred← citeshttps://doi.org/10.1093/nar/gkac1115openalex-snapshot
Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes
inferred← citeshttps://doi.org/10.1093/nargab/lqad004openalex-snapshot
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
inferred← citeshttps://doi.org/10.1101/2020.02.25.964445openalex-snapshot
SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing
inferred← citeshttps://doi.org/10.1101/2020.04.17.035287openalex-snapshot
RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
inferred← citeshttps://doi.org/10.1101/2020.05.07.082347openalex-snapshot
Third generation indexing for third generation sequencing
inferred← citeshttps://doi.org/10.1101/2021.01.28.428549openalex-snapshot
Strobemers: an alternative to k-mers for sequence comparison
inferred← citeshttps://doi.org/10.1101/2021.06.09.447586openalex-snapshot
Minimizer-space de Bruijn graphs
inferred← citeshttps://doi.org/10.1101/2021.06.18.449070openalex-snapshot
Flexible seed size enables ultra-fast and accurate read alignment
inferred← citeshttps://doi.org/10.1101/2022.01.11.475870openalex-snapshot
Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances
inferred← citeshttps://doi.org/10.1101/2022.05.21.492932openalex-snapshot
A survey of mapping algorithms in the long-reads era
inferred← citeshttps://doi.org/10.1101/2022.06.08.495395openalex-snapshot
A pan-genome approach to decipher variants in the highly complex tandem repeat of LPA
inferred← citeshttps://doi.org/10.1101/2022.08.27.505549openalex-snapshot
Genome assembly of the acoel flatworm Symsagittifera roscoffensis , a model for research on photosymbiosis
inferred← citeshttps://doi.org/10.1101/2022.09.06.506758openalex-snapshot
Genome assembly with variable order de Bruijn graphs
inferred← citeshttps://doi.org/10.1101/2023.01.16.524251openalex-snapshot
PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793
inferred← citeshttps://doi.org/10.1101/2023.04.18.537422openalex-snapshot
Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes
inferred← citeshttps://doi.org/10.1101/2023.10.19.563028openalex-snapshot
VRP Assembler: haplotype-resolved de novo assembly of diploid and polyploid genomes using quantum computing
inferred← citeshttps://doi.org/10.1101/2024.03.01.582926openalex-snapshot
High-fidelity annotated genome of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii
inferred← citeshttps://doi.org/10.1101/2024.04.15.589623openalex-snapshot
ModDotPlot - Rapid and interactive visualization of complex repeats
inferred← citeshttps://doi.org/10.1101/2024.10.18.619002openalex-snapshot
Using readmers and hapmers in assessing phase switching after read error correction of Oxford Nanopore Sequences
inferred← citeshttps://doi.org/10.1101/2025.09.29.679204openalex-snapshot
Fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching: the Alice assembler
inferred← citeshttps://doi.org/10.1101/810341openalex-snapshot
Accurate chromosome-scale haplotype-resolved assembly of human genomes
inferred← citeshttps://doi.org/10.1101/gr.263566.120openalex-snapshot
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
inferred← citeshttps://doi.org/10.1101/gr.275648.121openalex-snapshot
Effective sequence similarity detection with strobemers
inferred← citeshttps://doi.org/10.1101/gr.277334.122openalex-snapshot
Gaps and complex structurally variant loci in phased genome assemblies
inferred← citeshttps://doi.org/10.1101/gr.277645.123openalex-snapshot
Entropy predicts sensitivity of pseudorandom seeds
inferred← citeshttps://doi.org/10.1101/gr.277651.123openalex-snapshot
Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash
inferred← citeshttps://doi.org/10.1126/science.abf7117openalex-snapshot
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
inferred← citeshttps://doi.org/10.1128/mra.00610-25openalex-snapshot
High-quality draft genome sequence of the tropical lichen-forming fungus Lecanora helva (Lecanoraceae, Ascomycota)
inferred← citeshttps://doi.org/10.1146/annurev-pharmtox-051921-091209openalex-snapshot
Pharmacogenomics Beyond Single Common Genetic Variants: The Way Forward
inferred← citeshttps://doi.org/10.1186/s13059-020-02206-wopenalex-snapshot
Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
inferred← citeshttps://doi.org/10.1186/s13059-020-1935-5openalex-snapshot
Opportunities and challenges in long-read sequencing data analysis
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Computational methods for chromosome-scale haplotype reconstruction
inferred← citeshttps://doi.org/10.1186/s13059-021-02430-yopenalex-snapshot
Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
inferred← citeshttps://doi.org/10.1186/s13059-022-02831-7openalex-snapshot
Strobealign: flexible seed size enables ultra-fast and accurate read alignment
inferred← citeshttps://doi.org/10.1186/s13059-023-02972-3openalex-snapshot
A survey of mapping algorithms in the long-reads era
inferred← citeshttps://doi.org/10.1186/s13059-024-03414-4openalex-snapshot
When less is more: sketching with minimizers in genomics
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Emerging trends in pharmacogenomics: from common variant associations toward comprehensive genomic profiling
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A draft sequence reference of the Psilocybe cubensis genome
inferred← citeshttps://doi.org/10.12688/f1000research.51613.2openalex-snapshot
A draft reference assembly of the Psilocybe cubensis genome
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Twelve quick steps for genome assembly and annotation in the classroom
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Using de novo assembly to identify structural variation of eight complex immune system gene regions
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Computational Methods for Chromosome-Scale Haplotype Reconstruction
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VRP Assembler: Haplotype-Resolved de novo Assembly of Diploid and Polyploid Genomes Using Quantum Computing
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A deep dive into genome assemblies of non-vertebrate animals
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What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout
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Genome assembly of Parapercis colias (Blue cod/Rāwaru); An endemic marine fish species of New Zealand
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Challenges in the detection and assembly of virus integration structures in human genomes
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A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data
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Rethinking DeepVariant: Efficient Neural Architectures for Intelligent Variant Calling
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Faculty Opinions recommendation of Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
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Robust haplotype-resolved assembly of diploid individuals without parental data
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XPCLRS: fast selection signature detection using cross-population composite likelihood ratio
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Novel components at the periphery of long read genome assembly tools
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