ArticleBioinformatics (Oxford, England)2024
AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.
Article in Bioinformatics (Oxford, England), 2024. 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene.Plant biotechnology journal · 2026Article
- A chromosome-scale genome assembly of Tigridiopalma magnifica.Scientific data · 2026Article
- Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.Journal of experimental botany · 2026Article
- Ten quick tips for using the NIH Comparative Genomics Resource.PLoS computational biology · 2026Article
- A chromosome-scale assembly of Ormosia boluoensis (Fabaceae).Scientific data · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Haplotyped genome mapping and functional characterization of a blueberry anthocyanin acetyltransferase (AAT) controlling the accumulation of acylated anthocyanins.Journal of experimental botany · 2025Article
- Chromosome-scale assemblies of three Ormosia species: repetitive sequences distribution and structural rearrangement.GigaScience · 2025Article
- VueGen: automating the generation of scientific reports.Bioinformatics advances · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
summaryGenome assembly projects have grown exponentially due to breakthroughs in sequencing technologies and assembly algorithms. Evaluating the quality of genome assemblies is critical to ensure the reliability of downstream analysis and interpretation. To fulfil this task, we have developed the AssemblyQC pipeline that performs file-format validation, contaminant checking, contiguity measurement, gene- and repeat-space completeness quantification, telomere inspection, taxonomic assignment, synteny alignment, scaffold examination through Hi-C contact-map visualization, and assessments of completeness, consensus quality and phasing through k-mer analysis. It produces a comprehensive HTML report with method descriptions, tables, and visualizations. AVAILABILITY AND IMPLEMENTATION: The pipeline uses Nextflow for workflow orchestration and adheres to the best-practice established by the nf-core community. This pipeline offers a reproducible, scalable, and portable method to assess the quality of genome assemblies-the code is available online at GitHub: https://github.com/Plant-Food-Research-Open/assemblyqc.
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.