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bio-long-read-sequencing-nanopore-methylation
Maintainer FreedomIntelligence · Last updated April 1, 2026
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-long-read-sequencing-nanopore-methylation
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- CLI: modkit pileup aligned.bam methylation.bed --ref ref.fa.
- Call methylation from my Nanopore reads" → Extract 5mC/6mA modification probabilities from basecalled reads and summarize per-site methylation frequencies. CLI: modkit pileup aligned.bam methylation.bed --ref ref.fa.
- modkit pileup input.bam methylation.bed \ --ref reference.fa \ --cpg \ --combine-strands.
Source Doc
Excerpt From SKILL.md
Modern Workflow (modkit)
ONT's modkit is the recommended tool for methylation analysis from basecalled data.
bedMethyl format
chr1 1000 1001 . 10 + 1000 1001 0,0,0 10 80.5
Dorado basecalling with 5mC model
dorado basecaller [email protected]
pod5_dir/
--modified-bases 5mCG
> calls.bam
Use cases
- Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- long-read-sequencing/basecalling - Dorado basecalling
- methylation-analysis/methylation-calling - General methylation concepts
- methylation-analysis/dmr-detection - Differential methylation
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