Merqury: Reference-free Quality, Completeness, and Phasing Assessment for Genome Assemblies

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2020 Sep 15

PMID 32928274

Citations 1065

Authors

Arang Rhie

Brian P Walenz

Sergey Koren

Adam M Phillippy

Affiliations

Soon will be listed here.

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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