ArticleGigaByte (Hong Kong, China)2021
Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies.
Article in GigaByte (Hong Kong, China), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- A Forward Genetic Screen inbioRxiv : the preprint server for biology · 2026Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- BonoboFlow: viral genome assembly and haplotype reconstruction from nanopore reads.Bioinformatics advances · 2025Article
- Three Rounds of Read Correction Significantly Improve Eukaryotic Protein Detection in ONT Reads.Microorganisms · 2024Article
- Identifying transgene insertions inPeerJ · 2024Article
- Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms.Molecular biology and evolution · 2023Article
- Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing.Clinical epigenetics · 2022Review
- Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil.Microbiology resource announcements · 2022Article
- Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies.GigaByte (Hong Kong, China) · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for
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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.