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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Vydané v:	Genome Biology Ročník 21; číslo 1; s. 245
Hlavní autori:	Rhie, Arang, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M.
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	London BioMed Central 14.09.2020 Springer Nature B.V BMC
Predmet:	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
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Shrnutí:	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.
Bibliografia:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 ObjectType-Undefined-3
ISSN:	1474-760X 1474-7596 1474-760X
DOI:	10.1186/s13059-020-02134-9