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

Rhie, A.; Walenz, B. P.; Koren, S.; Phillippy, A. M.

doi:10.1101/2020.03.15.992941

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bioRxiv · 10.1101/2020.03.15.992941

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

Rhie, A.·Walenz, B. P.·Koren, S.·Phillippy, A. M.

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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. Availability of data and materialProject 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

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Rhie, A., Walenz, B. P., Koren, S., Phillippy, A. M.. 2020-03-17. Merqury: reference-free quality and phasing assessment for genome assemblies. https://doi.org/10.1101/2020.03.15.992941

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