“Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies” (2020), by Arang Rhie et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

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

Arang Rhie, Brian P. Walenz, Sergey Koren et al. · September 14, 2020 · Genetics and Biochemistry

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.

Free PDF DOI: 10.1186/s13059-020-02134-9