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 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. Availability of data and material Project name: Merqury Project home page: https://github.com/marbl/merqury , https://github.com/marbl/meryl Archived version: https://github.com/marbl/merqury/releases/tag/v1.0 Operating system(s): Platform independent Programming language: C++, Java, Perl Other requirements: gcc 4.8 or higher, java 1.6 or higher License: Public domain (see https://github.com/marbl/merqury/blob/master/README.license ) Any restrictions to use by non-academics: No restrictions applied