name: bio-long-read-sequencing-medaka-polishing description: 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 Covers the model-matching footgun that silently degrades output, why Racon-first is obsolete and medaka runs directly on Flye output as a single pass, why HiFi must never be fed to medaka, the v1-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. origin: openai4s category: bioskills/long-read-sequencing metadata: tool_type: cli primary_tool: medaka third_party: name: GPTomics/bioSkills repository: https://github.com/GPTomics/bioSkills commit: d91ed3d563019e649dc854c56ccd62551359488a license: MIT
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.
"Polish my Nanopore assembly" -> Run one medaka consensus pass directly on the assembler output, with the model that matches the basecaller - because a mismatched model silently makes the consensus worse.
- CLI: medaka_consensus -i reads.fq -d draft.fa -o out/ -t 8 (model auto-detected from the basecaller annotation)
medaka is an Oxford Nanopore tool. For PacBio (HiFi/CLR) it is the wrong tool entirely - route to genome-assembly/assembly-polishing.
medaka is a basecaller-model-specific neural consensus net trained on one exact stack (pore + motor enzyme + speed + basecaller mode + basecaller version). Three consequences:
medaka tools resolve_model --auto_model consensus reads.bam); treat a stale model name as a reason to re-basecall, not to proceed.| Mode | Input | medaka's role |
|---|---|---|
| Assembly polishing | Flye/Canu draft + ONT reads | raise per-base QV (homopolymer-indel cleanup is the dominant win) |
| Haploid variant calling | ONT reads + reference (microbial, mito, viral) | medaka_variant wrapper -> haploid VCF (apply with bcftools consensus for a FASTA) |
| Amplicon / viral consensus | tiling-amplicon ONT reads | the non-signal consensus arm of ARTIC fieldbioinformatics / EPI2ME wf-artic |
| Scenario | Recommended | Why |
|---|---|---|
| ONT-only Flye/Canu assembly | medaka_consensus, ONE pass, auto-detected model |
model-matched consensus; racon pre-step is obsolete |
| Native bacterial isolate (modified DNA) | medaka_consensus --bacteria |
bacterial-methylation model fixes methylation-motif errors |
| ONT small-variant (diploid/germline) calling | -> clair3-variants | medaka diploid calling deprecated in v2 (Clair3 surpassed it) |
| Haploid microbial/mito/viral VCF | medaka_variant (the renamed haploid wrapper) |
still supported in v2 |
| Read-level / human polishing | dorado polish |
ONT's emerging successor; identical bacterial weights to medaka today |
| PacBio HiFi/CLR | -> genome-assembly/assembly-polishing | medaka has no PacBio models; never ONT-polish HiFi |
| Unsure which basecaller model produced the reads | re-basecall, then auto-detect | a guessed model silently degrades the consensus |
The wrapper runs three steps: align (mini_align, a thin veil over minimap2 -x map-ont), infer (medaka inference, the neural net over the pileup), and stitch (medaka sequence, regions -> consensus FASTA).
# Canonical modern usage - model auto-detected from the basecaller annotation in the reads
medaka_consensus -i reads.fastq -d draft.fa -o medaka_out/ -t 8
# medaka_out/consensus.fasta is the polished assembly
# Native bacterial isolate: use the methylation-aware bacterial model
medaka_consensus -i reads.fastq -d draft.fa -o medaka_out/ -t 8 --bacteria
# Resolve / list models (do this when auto-detection cannot pick)
medaka tools resolve_model --auto_model consensus reads.bam
medaka tools list_models
medaka runs directly on the assembler (Flye) output as a SINGLE pass - do NOT pre-run Racon (contemporary models are trained on raw assembler output; v2 removed the bundled racon wrapper) and do NOT run medaka twice (iteration was racon's role; a second pass risks flipping correct bases).
medaka_variant emits a VCF only (no consensus FASTA); apply it to the reference with bcftools consensus to get a haploid consensus sequence.
# Wrapper form (renamed from medaka_haploid_variant in v2) - haploid samples only
medaka_variant -i reads.fastq -r reference.fa -o variant_out/
# Manual form - note v2 subcommand names and the hdf -> ref -> out argument order
minimap2 -ax map-ont reference.fa reads.fq | samtools sort -o aln.bam && samtools index aln.bam
medaka inference aln.bam probs.hdf --model r1041_e82_400bps_sup_variant_v5.0.0
medaka vcf probs.hdf reference.fa variants.vcf
# Optional: turn the VCF into a haploid consensus FASTA
bgzip variants.vcf && tabix -p vcf variants.vcf.gz
bcftools consensus -f reference.fa variants.vcf.gz > consensus.fasta
Trigger: running medaka with a model that does not match the basecaller chemistry/version. Mechanism: the net corrects toward the wrong error fingerprint. Symptom: lower held-out QV; medaka exits 0 with no warning. Fix: auto-detect from the BAM; if forced to pick, derive from the actual basecaller and confirm in list_models; treat a stale name as a reason to re-basecall.
Trigger: polishing a PacBio assembly with medaka. Mechanism: ONT-only error model, no PacBio support, on already-QV40+ data. Symptom: degraded/homogenized consensus. Fix: do not; route to genome-assembly/assembly-polishing.
Trigger: running Racon before medaka out of habit. Mechanism: contemporary models are trained on raw assembler output; racon-polished input is off the training distribution. Symptom: no gain or mild harm. Fix: run medaka directly on the Flye output; one pass.
Trigger: an assembly missing a small replicon (~80% identical to a chromosomal region). Mechanism: the absent plasmid's reads misalign onto the chromosome, and medaka "corrects" toward that spurious evidence. Symptom: clustered changes that introduce real errors. Fix: make the assembly structurally complete first; inspect medaka's changes for clustering (clustered = mapping artifact, not scattered homopolymer fixes).
Trigger: judging the polish by medaka's change count or by re-mapping the same reads. Mechanism: medaka optimizes agreement with its input pileup. Symptom: "improvement" that is circular. Fix: reference-free Merqury QV before vs after on held-out / different-platform k-mers.
| Threshold | Source | Rationale |
|---|---|---|
| 1 medaka pass | medaka README | a single trained-model pass; iteration was racon's role, extra passes flip correct bases |
| model must match basecaller version | medaka model design | mismatch silently degrades; the #1 ONT-polishing error |
| inference threads ~2 | medaka inference behavior | the net is GPU-bound and scales poorly past ~2 CPU threads |
| HiFi QV40+ already | EBP/HiFi baseline | nothing for an ONT consensus net to gain; only harm |
| measure with held-out Merqury QV | Rhie 2020 | the only honest, reference-free before/after instrument |
| Error / symptom | Cause | Solution |
|---|---|---|
medaka consensus not found / wrong args |
v1 subcommand renamed | use medaka inference (or the medaka_consensus wrapper) |
medaka stitch / medaka variant fail |
v1 names | medaka sequence / medaka vcf |
| Polished assembly worse than draft | model mismatch | auto-detect the model; re-basecall if the model is stale |
| medaka errors on PacBio reads | no PacBio models | route to genome-assembly/assembly-polishing |
| Clustered, suspicious changes | missing/mis-structured contig in the draft | complete the assembly first; filter to high-identity alignments |
| Looking for diploid SNP calling | deprecated in v2 | use clair3-variants |