Polishing

• Polishing the Final Assembly
  • Generate Haplotype Specific References
  • Align ONT, HiFi, and Illumina reads
  • Create a hybrid alignment (HiFi and Illumina combined)
  • Run DeepVariant in different modes depending on the reference type
  • Build HiFi-illumina hybrid meryl Db and get the haploid coverage
  • Filter variants precisely to retain only true variants
  • Build a new consensus using the true variant set
  • (Optional but Recommended) Perform quality checks on the new assembly
  • References