ArticleGenome biology2020
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,509 papers.
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2,509 citing papers in PubMed.
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- A chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica.The Journal of heredity · 2026Article
- Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.G3 (Bethesda, Md.) · 2026Article
- Genome evolution and long-term demographic history in true crocodiles.G3 (Bethesda, Md.) · 2026Article
- De Novo Assembly of the Trypanosoma congolense Genome Reveals an Organization Influenced by Antigenic Variation but Distinct from Trypanosoma brucei.Genome biology and evolution · 2026Article
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4 authors.
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Abstract
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations. By comparing k-mers in a de novo assembly to those found in unassembled high-accuracy reads, Merqury estimates base-level accuracy and completeness. For trios, Merqury can also evaluate haplotype-specific accuracy, completeness, phase block continuity, and switch errors. Multiple visualizations, such as k-mer spectrum plots, can be generated for evaluation. We demonstrate on both human and plant genomes that Merqury is a fast and robust method for assembly validation.
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