ArticleNature communications2023
Linear time complexity de novo long read genome assembly with GoldRush.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
- Hash functions in nucleotide sequence analysis.Genome research · 2026Review
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- Time-Efficient and Informatic-Skill-Light Gap-Filling for Telomere-to-Telomere Genome Assembly.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
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- ConSeqUMI, an error-free nanopore sequencing pipeline to identify and extract individual nucleic acid molecules from heterogeneous samples.Nucleic acids research · 2025Article
- A high-quality Oxford Nanopore assembly of the hourglass dolphin (Lagenorhynchus cruciger) genome.G3 (Bethesda, Md.) · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- GoldPolish-target: targeted long-read genome assembly polishing.BMC bioinformatics · 2025Article
- ntRoot: computational inference of human ancestry at scale from genomic data.Bioinformatics advances · 2025Article
- Genome Assembly by a Non-bioinformatician: Case Study of a Small Predatory Natural Enemy Insect, Nesidiocoris tenuis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Sexual dimorphism in the tardigrade Paramacrobiotus metropolitanus transcriptome.Zoological letters · 2024Article
- Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.Microbial genomics · 2024Article
- Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies.bioRxiv : the preprint server for biology · 2024Article
- Article
- Comparative Genomic Analysis ofJournal of fungi (Basel, Switzerland) · 2023Article
- Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.Molecular diagnosis & therapy · 2023Review
- Linear time complexity de novo long read genome assembly with GoldRush.Nature communications · 2023Article
- Genome ofFrontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Current state-of-the-art de novo long read genome assemblers follow the Overlap-Layout-Consensus paradigm. While read-to-read overlap - its most costly step - was improved in modern long read genome assemblers, these tools still often require excessive RAM when assembling a typical human dataset. Our work departs from this paradigm, foregoing all-vs-all sequence alignments in favor of a dynamic data structure implemented in GoldRush, a de novo long read genome assembly algorithm with linear time complexity. We tested GoldRush on Oxford Nanopore Technologies long sequencing read datasets with different base error profiles sourced from three human cell lines, rice, and tomato. Here, we show that GoldRush achieves assembly scaffold NGA50 lengths of 18.3-22.2, 0.3 and 2.6 Mbp, for the genomes of human, rice, and tomato, respectively, and assembles each genome within a day, using at most 54.5 GB of random-access memory, demonstrating the scalability of our genome assembly paradigm and its implementation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.