Bio Basecalling
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado...
Install
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -g -a claude-code -y- Repository
- FreedomIntelligence/OpenClaw-Medical-Skills3.1k
- Category
- Engineering
- Updated
- 4mo ago
- License
- See repository
- Context cost
- Mediumabout 1,944 tokens
- Runs scripts
- Yes, review before use
What it does
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.
Version Compatibility
Reference examples tested with: samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto 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.
Nanopore Basecalling
"Basecall my Nanopore data" → Convert raw electrical signal (FAST5/POD5) into nucleotide sequences with quality scores, optionally detecting modified bases.
- CLI:
dorado basecaller sup pod5/ > calls.bam(recommended),dorado basecaller sup,5mCG_5hmCG pod5/(with modifications)
Convert raw electrical signal from Nanopore sequencing into nucleotide sequences.
Dorado (Recommended)
Dorado is ONT's current production basecaller, replacing Guppy. It offers better accuracy and speed.
Basic Basecalling
dorado basecaller sup pod5_dir/ > calls.bam
Choose Model
dorado basecaller fast pod5_dir/ > calls.bam
dorado basecaller hac pod5_dir/ > calls.bam
dorado basecaller sup pod5_dir/ > calls.bam
Model Speed vs Accuracy
| Model | Speed | Accuracy | Use Case |
|---|---|---|---|
| fast | Fastest | Lower | Quick preview |
| hac | Medium | High | General use |
| sup | Slowest | Highest | Publication quality |
Specific Model Version
dorado download --model dna_r10.4.1_e8.2_400bps_sup@v5.1.0
dorado basecaller dna_r10.4.1_e8.2_400bps_sup@v5.1.0 pod5_dir/ > calls.bam
List Available Models
dorado download --list
Output FASTQ Instead of BAM
dorado basecaller sup pod5_dir/ --emit-fastq > calls.fastq
Modified Base Detection
dorado basecaller sup,5mCG_5hmCG pod5_dir/ > calls_mods.bam
dorado basecaller sup,5mCG pod5_dir/ > calls_5mc.bam
dorado basecaller sup,6mA pod5_dir/ > calls_6ma.bam
