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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.

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. Overall assembly evaluation

1. Reference free QV estimate
2. k-mer completeness (recovery rate)
3. Spectra copy number analysis
4. Track error bases in the assembly

3. Phasing assessment with hap-mers

1. Hap-mer completeness (recovery rate) and blob plots
2. Spectra copy number analysis per hap-mers
3. Phase block statistics and switch error rates
4. Track each haplotype block in the assembly