ArticleNature biotechnology2020
Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.
Article in Nature biotechnology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 321 papers.
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Who cites it
321 citing papers in PubMed.
- Complete assembly of Onobrychis viciifolia mitochondrial genome reveals evolutionary dynamics.Planta · 2026Article
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- Museum Genomics of an Important Swedish Pollinator Reveals Population Stability Across Time.Molecular ecology · 2026Article
- Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.Genome research · 2026Article
- Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer.Nature communications · 2026Article
- VCboost: reducing false positives in long-read variant calling for single-nucleotide polymorphism and indel detection in challenging genomic regions.Briefings in bioinformatics · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
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- Biosensing With Nanofluidics.Exploration (Beijing, China) · 2026Review
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- New genomic insights into long-chain alkenone biosynthesis by the coccolithophorid marine alga Gephyrocapsa huxleyi.BMC genomics · 2026Article
- A reference genome for cultured Drosophila ovarian somatic cells enables studies of transposon and piRNA biology.Genome biology · 2026Article
- Genome sequence of the ornamental plant Digitalis purpurea reveals the molecular basis of flower color and morphology variation.BMC genomics · 2026Article
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- Oxford nanopore technology R10 improved assembly metrics of Borrelia plasmids compared to R9.BMC genomics · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
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- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Cookbook for plant genome sequences.BMC genomics · 2026Review
261 more citing papers are in PubMed but not listed here.
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32 authors.
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Abstract
De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.
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