Downloader

Dorado can download models from the Oxford Nanopore Content Delivery Network (CDN) using the Dorado download command.

❯ dorado download --help

Usage: dorado [--help]
    [--model (<model_name>|"all")]
    [--models-directory PATH]
    [--list] [--list-yaml] [--list-structured]
    [--data VAR] [--recursive] [--overwrite] [--verbose]...

Optional arguments:
  -h, --help          shows help message and exits
  --model             the model to download [nargs=0..1] [default: "all"]
  --models-directory  the directory to download the models into [nargs=0..1] [default: "."]
  --list              list the available models for download
  --list-yaml         list the available models for download, as yaml, to stdout
  --list-structured   list the available models in a structured format, as yaml, to stdout
  --data              path to POD5 data used to automatically select models [nargs=0..1] [default: ""]
  -r, --recursive     recursively scan through directories to load POD5 files
  --overwrite         overwrite existing models if they already exist
  -v, --verbose       [may be repeated]

Downloading models

Download all models

To download all models use:

dorado download --model all

Download models for a specific condition

To download models for a specific sequencing condition and model speed, provide a variant model complex to the --model argument and set the --data argument to path to your pod5 input data (.fast5 is not supported).

Dorado will then download the simplex and modified base models matching the condition and model complex selection.

dorado download --model hac --data pod5s/

Download specific models

To find and download a specific model use the following command to view a list of all available models. These are also noted in the Models List below.

dorado download --list

which shows an output like this where model names are printed for each model type

> simplex models
 - dna_r10.4.1_e8.2_400bps_hac@v5.2.0
 - dna_r10.4.1_e8.2_400bps_sup@v5.2.0
 ...
> modification models
 - dna_r10.4.1_e8.2_400bps_hac@v5.2.0_6mA@v1
 ...

The models can then be downloaded using their model name as shown below

dorado download --model <model_name>

Download models into a specific directory

By default Dorado download will download models into the current working directory. Use the --models-directory argument to specify a directory to save downloaded models into.

See also model discovery for details on how previously downloaded models are found or automatically downloaded.

dorado download --model <model_name> --models-directory /path/to/models_directory

Tip

The --models-directory argument is available on many Dorado commands (e.g. basecaller) to specify a directory to search for existing models. This can be used to avoid repeatedly downloading models.