Purpose

Merqury allows a 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.

Input

Merqury requires two types of inputs: meryldbs and the genome assemblies. There is no need to run merqury per-assemblies. If two assemblies areprovided, Merqury generates stats for each and combined.

Output

The generated metrics include consensus quality and k-mer completeness, and when parental genomic sequences are available (either assembled or unassembled), Merqury can output haplotype completeness, phase block statistics, switch error rates, and visual representations of phase consistency for the child’s genome. This includes TDF (or BED) features that can be displayed in a genome browser for visualizing the presence of k-mer classes across a genome (e.g., the k-mers inherited from a parental genome).

You can add column headers to the completeness and qv outputs by checking the option "Add column header on tabular outputs".