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Merqury

Merqury provides a set of tools for reference free assembly evaluation.
Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference.

Features

1. Evaluate assemblies

   • Reference free QV estimate
   • k-mer completeness (recovery rate)
   • Spectra copy number spectrum
   • Tracks for erroneous k-mers (bases) in the assembly

2. Assess phasing completeness

   • Hap-mer completeness (recovery rate) and blob plots
   • Spectra copy number analysis per hap-mers
   • Phase block statistics and switch error rates
   • Phased block tracks for each haplotype in the assembly

1. Prepare meryl dbs

1. Get the right k size
2. Build k-mer dbs with meryl
3. Build hap-mers for trios

For more details, see this page.

2. Analysis

1. Overall assembly evaluation
2. Phasing assessment with hap-mers