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medaka-polishing

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Polishes Oxford Nanopore draft assemblies to higher consensus accuracy with medaka, a basecaller-model-specific neural consensus net, produces haploid variant calls (VCF) for microbial, mitochondrial, or viral samples, and generates amplicon/viral consensus sequences. Covers the model-matching footgun that silently degrades output, why Racon-first is obsolete and medaka runs directly on Flye output as a single pass, why HiFi must never be fed to medaka, the v1->v2 subcommand renames, and the precise medaka_variant deprecation. Use when polishing an ONT-only assembly, generating an amplicon/viral consensus, calling a haploid ONT consensus, or deciding whether medaka, dorado polish, or Clair3 is the right tool.

When to use

• Polishing an ONT-only assembly
• Generating an amplicon/viral consensus
• Calling a haploid ONT consensus
• Deciding whether medaka, dorado polish, or Clair3 is the right tool
• Haploid microbial/mito/viral VCF
• Native bacterial isolate polishing

When not to use

• PacBio HiFi/CLR polishing
• ONT small-variant (diploid/germline) calling
• Read-level / human polishing

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