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bio-long-read-sequencing-nanopore-methylation
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-long-read-sequencing-nanopore-methylation
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- CLI：modkit pileup aligned.bam methylation.bed --ref ref.fa。
- Call methylation ，面向 my Nanopore reads" → Extract 5mC/6mA modification probabilities ，面向 basecalled reads 、 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。
原始文档
SKILL.md 摘录
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
适用场景
- 适合在detecting 5mC 或 6mA modifications directly ，面向 nanopore reads without bisulfite conversion时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- long-read-sequencing/basecalling - Dorado basecalling
- methylation-analysis/methylation-calling - General methylation concepts
- methylation-analysis/dmr-detection - Differential methylation
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