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README.md

Dorado container

Main tool: dorado

Code repository: https://github.com/nanoporetech/dorado

Basic information on how to use this tool:

  • executable: dorado
  • help: -h, --help
  • version: -v, --version
  • description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Additional information:

  • This container does not contain any models. The models can be downloaded manually by dorado download command. If no specific model is provided, Dorado will automatically select and download the appropriate one using the model selection complex.
  • Cuda drivers >= 12.2.0 are required for gpu support.
  • Use "--gpus all" flag to activate gpu support in docker. E.g. docker run -it --gpus all staphb/dorado:1.1.0-cuda12.2.0-no_model bash
  • Support for Fast5 files and basecalling models for DNA R10.4.1 4kHz data, DNA R9.4.1, and RNA002 were removed after v0.9.6

Full documentation: https://dorado-docs.readthedocs.io/en/latest/

Example Usage

# list models
dorado download --list
# download a single model
dorado download --model {model_name}
# download all models
dorado download
# basecaller
dorado basecaller {model} {data} > calls.bam