Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.
Assembly validation
Benchmarking
Genome assembly
Haplotype phasing
K-mers
Trio binning
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
14 09 2020
14 09 2020
Historique:
received:
31
03
2020
accepted:
06
08
2020
entrez:
15
9
2020
pubmed:
16
9
2020
medline:
12
6
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32928274
doi: 10.1186/s13059-020-02134-9
pii: 10.1186/s13059-020-02134-9
pmc: PMC7488777
doi:
Types de publication
Journal Article
Research Support, N.I.H., Intramural
Validation Study
Langues
eng
Sous-ensembles de citation
IM
Pagination
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