Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

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 thos...

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Bibliographic Details
Published in:Genome Biology Vol. 21; no. 1; p. 245
Main Authors: Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.
Format: Journal Article
Language:English
Published: London BioMed Central 14.09.2020
Springer Nature B.V
BMC
Subjects:
Accuracy
Animal Genetics and Genomics
Arabidopsis
Assembly validation
Benchmarking
Bioinformatics
Biomedical and Life Sciences
Evolutionary Biology
genome
Genome assembly
Genome, Human
Genome, Plant
Genomes
Genomics - methods
Haplotype phasing
Haplotypes
Human Genetics
Humans
K-mers
Life Sciences
Method
Microbial Genetics and Genomics
Plant Genetics and Genomics
planting
Software
Trio binning
Benchmarking
K-mers
Genome assembly
Haplotype phasing
Trio binning
Assembly validation
ISSN:1474-760X, 1474-7596, 1474-760X
Online Access:Get full text
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Summary: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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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02134-9