Individual skill
bio-long-read-sequencing-medaka-polishing
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 Covers the model-matching footgun that silently degrades output, why Racon-first is obsolete and medaka runs directly on Flye output as a single pass, why HiFi must never be fed to medaka, the v1-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.
skills/bioskills/bio-long-read-sequencing-medaka-polishing/SKILL.md
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SKILL.mdcore · 12,357 bytesSKILL.mdcore · 12,357 bytesSKILL.mdcore · 12,357 bytesSKILL.mdcore · 12,357 bytesreferences/usage-guide.mddoc · 4,308 bytesscripts/medaka_polish.shruns · 1,256 bytesscripts/medaka_variant.shruns · 1,092 bytes
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## Version Compatibility
Reference examples tested with: medaka 2.2+, minimap2 2.28+, samtools 1.19+.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags
Results depend on inputs that outlive the binary version - record them:
- The medaka MODEL must match the basecaller (pore + chemistry + speed + mode + version), e.g. `r1041_e82_400bps_sup_v5.2.0`. A mismatch silently degrades output. Prefer auto-detection from the BAM; verify with `medaka tools list_models`.
- Default models advance with each release (consensus `..._sup_v5.2.0`, variant `..._sup_variant_v5.0.0` at time of writing); confirm with `medaka tools list_models`.
- medaka v2 renamed subcommands (`consensus`->`inference`, `stitch`->`sequence`, `variant`->`vcf`) and moved the backend to PyTorch; v1 tutorials fail.
If code throws an error, introspect the installed tool (`medaka --help`, `medaka_consensus --help`) and adapt the example to the actual API rather than retrying.
