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Arang Rhie edited this page Feb 8, 2020
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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 (details)
- Get the right k size
- Build k-mer dbs with meryl
- Build hap-mers for trios
2. Overall assembly evaluation (details)
- Reference free QV estimate
- k-mer completeness (recovery rate)
- Spectra copy number analysis
- Track error bases in the assembly
3. Phasing assessment with hap-mers (details)
- Inherited hap-mer plots
- Hap-mer blob plots
- Hap-mer completeness (recovery rate)
- Spectra copy number analysis per hap-mers
- Phased block statistics and switch error rates
- Track each haplotype block in the assembly