ArticleGigaScience2020
Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
91 citing papers in PubMed, 1 synthesis or guideline pooled it, 171 citations in OpenAlex.
- A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution.The Journal of heredity · 2023Pooled it
- Long-read whole-genome sequencing dataset of microbial communities from industrially and municipally impacted freshwater wetlands in South Africa.Data in brief · 2026Article
- Read-mapping signatures for molecular characterization of transgenic DNA insertions in paired-end Illumina data.BMC biotechnology · 2026Article
- High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214Scientific data · 2026Article
- FuFiHLA: a tool for full-field HLA typing from long-read data.Bioinformatics (Oxford, England) · 2026Article
- Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications.Genome research · 2026Article
- Transcriptomic Regulation of Aquaporins During Seed Germination in the Marine SeagrassPlants (Basel, Switzerland) · 2026Article
- A chromosome-level, haplotype-resolved genome assembly for the barn owl, Tyto alba.GigaScience · 2026Article
- Long-read sequencing for cancer liquid biopsy: advancing precision oncology.Frontiers in oncology · 2026Review
- AI-driven CRISPR strategies in breast cancer: Organoid modeling, adaptive editing, and precision delivery.Iranian journal of basic medical sciences · 2026Review
- Challenges in the detection and assembly of virus integration structures in human genomes.Frontiers in oncology · 2026Review
- A hitchhiker's guide to modern, practical cyanobacterial taxonomy.Journal of phycology · 2025Article
- Genomic and epigenomic maps of mouse centromeres and pericentromeres.Nature communications · 2025Article
- Assembly of a high-quality Polypterus senegalus diploid genome.Genes & genomics · 2025Article
- High-quality genome assembly ofHorticulture research · 2025Article
- Genomic insights into Shigella species isolated from small ruminants and manure in the North West Province, South Africa.Applied microbiology and biotechnology · 2025Article
- FuFiHLA: A tool for Full-Field HLA typing from long reads data.bioRxiv : the preprint server for biology · 2025Article
- HTS and PCR Methods Are the Most Used in the Diagnosis of Aspergillosis: Advantages over Other Molecular Methods.Journal of fungi (Basel, Switzerland) · 2025Review
- Chromosome-Level Assembly and Annotation of the Grey Reef Shark (Carcharhinus amblyrhynchos) Genome.Genome biology and evolution · 2025Article
- Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.BMC genomics · 2025Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe availability of reference genomes has revolutionized the study of biology. Multiple competing technologies have been developed to improve the quality and robustness of genome assemblies during the past decade. The 2 widely used long-read sequencing providers-Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)-have recently updated their platforms: PacBio enables high-throughput HiFi reads with base-level resolution of >99%, and ONT generated reads as long as 2 Mb. We applied the 2 up-to-date platforms to a single rice individual and then compared the 2 assemblies to investigate the advantages and limitations of each.
resultsThe results showed that ONT ultralong reads delivered higher contiguity, producing a total of 18 contigs of which 10 were assembled into a single chromosome compared to 394 contigs and 3 chromosome-level contigs for the PacBio assembly. The ONT ultralong reads also prevented assembly errors caused by long repetitive regions, for which we observed a total of 44 genes of false redundancies and 10 genes of false losses in the PacBio assembly, leading to over- or underestimation of the gene families in those long repetitive regions. We also noted that the PacBio HiFi reads generated assemblies with considerably fewer errors at the level of single nucleotides and small insertions and deletions than those of the ONT assembly, which generated an average 1.06 errors per kb and finally engendered 1,475 incorrect gene annotations via altered or truncated protein predictions.
conclusionsIt shows that both PacBio HiFi reads and ONT ultralong reads had their own merits. Further genome reference constructions could leverage both techniques to lessen the impact of assembly errors and subsequent annotation mistakes rooted in each.
Indexed as
Identifiers
What OpenQuestion holds
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.