ArticleBMC genomics2020
GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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
54 citing papers in PubMed.
- Article
- ChromoMapperWeb: evaluate genome alignments and track assembly steps within an interactive graphic environment.Nucleic acids research · 2026Article
- PAQman: reference-free ensemble evaluation of long-read genome assemblies.G3 (Bethesda, Md.) · 2026Article
- From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.World journal of microbiology & biotechnology · 2026Review
- Carboxydotrophic Acetogenesis in Alkaline Conditions Results in Transient Formate Production by the Halo-Alkaliphilic Acetogen Haloacetibacter carboxydivorans Gen. Nov. sp. Nov.Environmental microbiology reports · 2026Article
- A high-quality chromosome level genome assembly of the South African indigenous Nguni goat (Capra hircus).Scientific data · 2026Article
- Autotrophic methylotrophy with no methanol dehydrogenase (MDH) in a strain of fluorescentPeerJ · 2026Article
- Genome Sequences of Three Polyporaceae Species (Polyporales, Basidiomycota) from South Korea.Mycobiology · 2026Article
- Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae.bioRxiv : the preprint server for biology · 2025Article
- A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector.Nature protocols · 2025Review
- A complete diploid human genome benchmark for personalized genomics.bioRxiv : the preprint server for biology · 2025Article
- Genomic epidemiology of enteropathogenic Escherichia coli in southwestern Nigeria.PLoS neglected tropical diseases · 2025Article
- Chromosome-level genome assembly of the Vermilion Snapper (Rhomboplites aurorubens).Scientific data · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): a resource for conservation and comparative genomics.G3 (Bethesda, Md.) · 2025Article
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Genome Evaluation Pipeline (GEP): a fully automated quality control tool for parallel evaluation of genome assemblies.Bioinformatics advances · 2025Article
- Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Snow alga Sanguina aurantia as revealed through de novo genome assembly and annotation.G3 (Bethesda, Md.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
backgroundGenome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic diversity and differences in gene expression across individuals and tissue types. Quality metrics for genome assemblies gauge both the completeness and contiguity of an assembly and help provide confidence in downstream biological insights. To compare quality across multiple assemblies, a set of common metrics are typically calculated and then compared to one or more gold standard reference genomes. While several tools exist for calculating individual metrics, applications providing comprehensive evaluations of multiple assembly features are, perhaps surprisingly, lacking. Here, we describe a new toolkit that integrates multiple metrics to characterize both assembly and gene annotation quality in a way that enables comparison across multiple assemblies and assembly types.
resultsOur application, named GenomeQC, is an easy-to-use and interactive web framework that integrates various quantitative measures to characterize genome assemblies and annotations. GenomeQC provides researchers with a comprehensive summary of these statistics and allows for benchmarking against gold standard reference assemblies.
conclusionsThe GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.
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.