bio-longread-medaka

name	bio-longread-medaka
description	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.
tool_type	cli
primary_tool	medaka

Medaka Polishing and Variant Calling

Basic Consensus Polishing

# Polish assembly with medaka
medaka_consensus -i reads.fastq.gz \
    -d draft_assembly.fa \
    -o medaka_output \
    -t 4 \
    -m r1041_e82_400bps_sup_v5.0.0

Variant Calling (Haploid)

# Call variants against reference (medaka v2.0+)
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 instead.

Step-by-Step Workflow (medaka v2.0+)

# 1. Align reads to reference/draft
minimap2 -ax map-ont reference.fa reads.fastq.gz | \
    samtools sort -o aligned.bam
samtools index aligned.bam

# 2. Run neural network inference
medaka inference aligned.bam consensus.hdf \
    --model r1041_e82_400bps_sup_v5.0.0 \
    --threads 2                          


medaka sequence consensus.hdf reference.fa polished.fa


medaka vcf reference.fa consensus.hdf variants.vcf