ReviewBMC bioinformatics2020
Toward a more holistic method of genome assembly assessment.
Review in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
17 citing papers in PubMed.
- Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.Functional & integrative genomics · 2026Review
- Genomic insights into specialized and primary metabolism gene clusters in methicillin-resistant Staphylococcus aureus from Egyptian community settings.BMC genomics · 2026Article
- From contiguity to accuracy: Validation-centered perspectives on bacterial genome assembly.Journal of microbiology (Seoul, Korea) · 2026Review
- Multiple hybridization events and repeated evolution of homoeologue expression bias in parthenogenetic, polyploid New Zealand stick insects.Molecular ecology · 2025Article
- Comparative Evaluation of Open-Source Bioinformatics Pipelines for Full-Length Viral Genome Assembly.Viruses · 2024Article
- Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles.bioRxiv : the preprint server for biology · 2024Article
- Whole-genome sequencing in medicinal plants: current progress and prospect.Science China. Life sciences · 2024Review
- Review
- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
- Chromosome-length genome assembly of Teladorsagia circumcincta - a globally important helminth parasite in livestock.BMC genomics · 2023Article
- Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research.BMC genomics · 2022Article
- Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes.GigaScience · 2022Article
- The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science.Frontiers in veterinary science · 2022Review
- Technical considerations in Hi-C scaffolding and evaluation of chromosome-scale genome assemblies.Molecular ecology · 2021Article
- Complete Genome Sequence of Two Deep-SeaMarine drugs · 2021Article
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundA key use of high throughput sequencing technology is the sequencing and assembly of full genome sequences. These genome assemblies are commonly assessed using statistics relating to contiguity of the assembly. Measures of contiguity are not strongly correlated with information about the biological completion or correctness of the assembly, and a commonly reported metric, N50, can be misleading. Over the years, multiple research groups have rejected the overuse of N50 and sought to develop more informative metrics.
resultsThis paper presents a review of problems that arise from relying solely on contiguity as a measure of genome assembly quality as well as current alternative methods. Alternative methods are compared on the basis of how informative they are about the biological quality of the assembly and how easy they are to use. A comprehensive method for using multiple metrics of measuring assembly quality is presented.
conclusionsThis study aims to report on the status of assembly assessment methods and compare them, as well as to offer a comprehensive method that incorporates multiple facets of quality assessment. Weaknesses and strengths of varying methods are presented and explained, with recommendations based on speed of analysis and user friendliness.
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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.