Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-longread-medaka

Maintainer FreedomIntelligence · Last updated April 1, 2026

Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore data without short-read polishing.

OpenClawNanoClawAnalysisReproductionbio-longread-medaka🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcpolish

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-longread-medaka

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

CLI: medaka_polisher -i reads.fq -d draft.fa -o polished.fa -m r1041_e82_400bps_sup_v5.0.0.
Polish my ONT assembly with medaka" → Use neural networks trained on specific basecaller models to correct assembly errors and call variants from Nanopore data. CLI: medaka_polisher -i reads.fq -d draft.fa -o polished.fa -m r1041_e82_400bps_sup_v5.0.0.
medaka_consensus -i reads.fastq.gz \ -d draft_assembly.fa \ -o medaka_output \ -t 4 \ -m r1041_e82_400bps_sup_v5.0.0.

Source Doc

Excerpt From SKILL.md

Call variants against reference

medaka_variant
-i reads.fastq.gz
-r reference.fa
-o output_dir
-m r1041_e82_400bps_sup_v5.0.0


Note: Diploid variant calling has been deprecated in medaka v2.0. For diploid samples, use [Clair3](https://github.com/HKU-BAL/Clair3) instead.

## Step-by-Step Workflow

**Goal:** Polish an ONT assembly or call variants using medaka's neural network models with explicit control over each step.

**Approach:** Align reads with minimap2, run medaka neural network inference on the alignment, then generate either a polished consensus or variant calls from the probability output.

```bash

## 1. Align reads to reference/draft

minimap2 -ax map-ont reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam