# Bio Basecalling

Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado...

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-basecalling -g -a gemini-cli -y`

## Description

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.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: 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.

# 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

```bash
dorado basecaller sup pod5_dir/ > calls.bam
```

### Choose Model

```bash
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

```bash
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

```bash
dorado download --list
```

### Output FASTQ Instead of BAM

```bash
dorado basecaller sup pod5_dir/ --emit-fastq > calls.fastq
```

### Modified Base Detection

```bash
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
```

### GPU Selection

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-basecalling/SKILL.md