bio-longread-medaka
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.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+, minimap2 2.26+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Medaka Polishing and Variant Calling **"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` ## Basic Consensus Polishing ```bash # 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) ```bash # 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/
- Version Compatibility
- Basic Consensus Polishing
- Variant Calling (Haploid)
- Step-by-Step Workflow
- List Available Models
- Common Models
- Choose Model Based on Basecaller
- Polish Region Only
- Multiple Rounds of Polishing
- Call Variants from Existing BAM
- Filter VCF Output
- Output Files
- Key Parameters
- GPU Acceleration
Polish assembly with medaka medaka_consensus -i reads.fastq.gz \ Call variants against reference medaka_variant \ minimap2 -ax map-ont reference.fa reads.fastq.gz | \ samtools sort -o aligned.bam samtools index aligned.bam medaka inference aligned.bam consensus.hdf \ medaka sequence consensus.hdf reference.fa polished.fa medaka vcf reference.fa consensus.hdf variants.vcf
What does the bio-longread-medaka skill do?
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.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-longread-medaka --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.