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Dorado Duplex

Wrapper for the ONT dorado duplex basecalling tool. This tool performs basecalling on both strands of a duplex read.

Version

Current version: 1.0.0 (First stable release)

For a detailed list of changes, see the CHANGELOG.md.

Installation

Dorado can be installed from the Nanopore GitHub repository:

# Clone the repository
git clone https://github.com/nanoporetech/dorado.git
cd dorado

# Build dorado (requires CMake and a C++ compiler)
mkdir build && cd build
cmake ..
make -j

# Add dorado to your PATH
export PATH=$PATH:$(pwd)/bin

For general information on how to use wrappers in Snakemake, please refer to the root README.md.

Usage

rule dorado_duplex:
    input:
        pod="path/to/pod5/file.pod5",
        reference="path/to/reference.fa"  # optional
    output:
        "path/to/output.bam"
    params:
        model="sup",
        gpu="all"
    threads: 8
    wrapper:
        "file://path/to/damlab-wrappers/dorado/duplex"

Parameters

  • model (str, optional): Model to use for basecalling (default: "sup")
  • models_directory (str, optional): Path to custom models directory
  • dorado_path (str, optional): Path to dorado executable (default: "dorado")
  • gpu (str, optional): GPU device to use (default: "all")
    • Can be "all" or specific device number

Input

  • pod: Path to POD5 file or directory (required)
  • reference: Path to reference file (optional)

Output

  • BAM file containing basecalled reads

Error Handling

The wrapper includes error handling for:

  • Missing input files
  • Invalid parameters
  • Dorado execution errors
  • Basecalling failures

License

This project is licensed under the MIT License - see the LICENSE file for details.

Authors

  • Will Dampier, PhD

Software Requirements