Gene

Engineering

Biology

Reference genome

Set (abstract data type)

Data mining

Computer science

Completeness (order theory)

Sequence assembly

Phaser

Computational biology

k-mer

Genetics

Transcriptome

Genome

Mathematics

Mathematical analysis

Programming language

Gene expression

Electrical engineering

Genome biology

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.

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