ArticleNature biotechnology2015
De novo assembly of a haplotype-resolved human genome.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Whole-genome sequencing of 3135 individuals representing the genetic diversity of the Japanese population.Journal of human genetics · 2026Article
- Chromosome-Scale Genome and Transcriptomic Analyses Reveal Differential Regulation of Terpenoid Secondary Metabolites inJournal of fungi (Basel, Switzerland) · 2024Article
- Evolutionary history and biological adaptation of Han Chinese people on the Mongolian Plateau.hLife · 2024Article
- T2T-YAO Reference Genome of Han Chinese - New Step in Advancing Precision Medicine in China.Genomics, proteomics & bioinformatics · 2023Article
- A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.BMC biology · 2022Article
- De novo phasing resolves haplotype sequences in complex plant genomes.Plant biotechnology journal · 2022Review
- Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia.Frontiers in medicine · 2022Article
- Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation.Nature communications · 2021Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping.Journal of personalized medicine · 2021Article
- An integrated personal and population-based Egyptian genome reference.Nature communications · 2020Article
- Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.Nature communications · 2020Article
- Opportunities and challenges in long-read sequencing data analysis.Genome biology · 2020Review
- Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants.Genome research · 2019Article
- Assessment of human diploid genome assembly with 10x Linked-Reads data.GigaScience · 2019Article
- Development of coupling controlled polymerizations by adapter-ligation in mate-pair sequencing for detection of various genomic variants in one single assay.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome.Genomics, proteomics & bioinformatics · 2019Article
- Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions.Nature communications · 2019Article
- Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562.Genome research · 2019Article
- Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.Nature communications · 2019Article
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Authors and funding
41 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.
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