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数据与复现
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bio-basecalling
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Guppy is deprecated; use Dorado for all new analyses.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-basecalling
- 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：dorado basecaller sup pod5/ > calls.bam (recommended)，dorado basecaller sup，5mCG_5hmCG pod5/ (，支持 modifications)。
- Basecall my Nanopore data" → Convert raw electrical signal (FAST5/POD5) into nucleotide sequences ，支持 quality scores，optionally detecting modified bases. CLI：dorado basecaller sup pod5/ > calls.bam (recommended)，dorado basecaller sup，5mCG_5hmCG pod5/ (，支持 modifications)。
- Convert raw electrical signal ，面向 Nanopore sequencing into nucleotide sequences。
- Dorado is ONT's current production basecaller，replacing Guppy. It offers better accuracy 、 speed。
原始文档
SKILL.md 摘录
Model Speed vs Accuracy
| Model | Speed | Accuracy | Use Case |
|---|---|---|---|
| fast | Fastest | Lower | Quick preview |
| hac | Medium | High | General use |
| sup | Slowest | Highest | Publication quality |
Guppy (Deprecated - Legacy Only)
Guppy is deprecated and no longer receiving updates. Use Dorado for all new analyses. Guppy examples below are only for maintaining legacy pipelines.
POD5 File Handling
POD5 is the new format replacing FAST5.
适用场景
- 适合在processing raw Nanopore data before alignment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-alignment - Align basecalled reads
- long-read-qc - QC after basecalling
- medaka-polishing - Polish using basecalled reads
- structural-variants - SV detection from long reads
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