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

Authors
  • Rhie, Arang1
  • Walenz, Brian P.1
  • Koren, Sergey1
  • Phillippy, Adam M.1
  • 1 National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA , Bethesda (United States)
Type
Published Article
Publication Date
Sep 14, 2020
Volume
21
Issue
1
Identifiers
DOI: 10.1186/s13059-020-02134-9
Source
Springer Nature
Keywords
License
Green

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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