ReviewPLoS computational biology2019
Modern technologies and algorithms for scaffolding assembled genomes.
Review in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed.
- Benchmarking of bioinformatics tools for the hybridComputational and structural biotechnology journal · 2025Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.G3 (Bethesda, Md.) · 2024Article
- Chromosome-Scale Genome Assembly of the Sheep-Biting LouseInternational journal of molecular sciences · 2024Article
- Whole-genome sequencing of Ganoderma boninense, the causal agent of basal stem rot disease in oil palm, via combined short- and long-read sequencing.Scientific reports · 2024Article
- Pasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.Nucleic acids research · 2024Article
- Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads.Frontiers in bioinformatics · 2024Article
- Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.bioRxiv : the preprint server for biology · 2023Article
- Hybridization of Atlantic puffins in the Arctic coincides with 20th-century climate change.Science advances · 2023Article
- Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions.Plants (Basel, Switzerland) · 2023Article
- A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization.GigaScience · 2022Article
- Molecular insights into high-altitude adaption and acclimatisation ofLife science alliance · 2022Article
- Integrating Genetic and Chromosome Maps ofInternational journal of molecular sciences · 2022Article
- Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review.Briefings in functional genomics · 2022Review
- SWALO: scaffolding with assembly likelihood optimization.Nucleic acids research · 2021Article
- Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus.Genome biology and evolution · 2021Article
- De novo assembly of a new Olea europaea genome accession using nanopore sequencing.Horticulture research · 2021Article
- Benchmarking of next and third generation sequencing technologies and their associated algorithms forMolecular medicine reports · 2021Article
- SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.BMC bioinformatics · 2021Article
- Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.Nature communications · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The computational reconstruction of genome sequences from shotgun sequencing data has been greatly simplified by the advent of sequencing technologies that generate long reads. In the case of relatively small genomes (e.g., bacterial or viral), complete genome sequences can frequently be reconstructed computationally without the need for further experiments. However, large and complex genomes, such as those of most animals and plants, continue to pose significant challenges. In such genomes, assembly software produces incomplete and fragmented reconstructions that require additional experimentally derived information and manual intervention in order to reconstruct individual chromosome arms. Recent technologies originally designed to capture chromatin structure have been shown to effectively complement sequencing data, leading to much more contiguous reconstructions of genomes than previously possible. Here, we survey these technologies and the algorithms used to assemble and analyze large eukaryotic genomes, placed within the historical context of genome scaffolding technologies that have been in existence since the dawn of the genomic era.
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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.