Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
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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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The assembly O.moschatus_RAN27-v1.0 has a completeness of 93.49% as determined by tabulation of k-mers derived from highly accurate Illumina short-reads using Merqury.
“The resulting assembly, O.moschatus_RAN27-v1.0, has a contig N50 of 44.7 Mbp, a scaffold N50 of 112.3 Mbp, and a completeness of 93.49% as determined by the tabulation of k-mers derived from highly accurate Illumina short-reads using Merqury50.”
From Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics (2024) · cites this paper as [50]
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“0, has a contig N50 of 44.7 Mbp, a scaffold N50 of 112.3 Mbp, and a completeness of 93.49% as determined by the tabulation of k-mers derived from highly accurate Illumina short-reads using Merqury 50 .”
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- Authors
- Rhie, A., Walenz, B. P., Koren, S., & Phillippy, A. M.
- Affiliations
- National Institutes of Health (US)
- Corresponding author
- Rhie, Arang
- Venue
- Genome Biology
- Published
- 2020-09-14
- Volume
- 21
- Issue
- 1
- Pages
- 245-245
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC7488777
- OpenAlex
- W3085758516
- Cited by
- 3,643
- References
- 51
- Citations by year
- 2026: 962 · 2025: 1057 · 2024: 851 · 2023: 551 · 2022: 152 · 2021: 56 · 2020: 13 · 2012: 1
- FWCI
- 63.03
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Human Genome Research Institute (Intramural Research Program)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- genome assembly evaluation, assembly completeness, assembly accuracy, haplotype phasing, trio analysis, long-read sequencing, human genome, plant genome
- MeSH terms
- Humans, Software, Genome, Human, Arabidopsis, Genome, Plant, Genomics
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