nanoporetech/dorado repository overview

⁠Dorado

Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

⁠Usage

Please refer to the dorado GitHub⁠ page for basic information regarding running dorado.

The docker images are built on top of the official nvidia/cuda⁠ images. They are suitable to be run on any host computer with a recent NVIDIA GPU driver and the NVIDIA Container Toolkit⁠.

The images contain basecaller configurations (models and meta information) within the container. The command list-models can be used to list the available options:

$ docker run nanoporetech/dorado list-models
/models/[email protected]
/models/[email protected]_5mCG@v2
/models/[email protected]
/models/[email protected]_5mCG@v2
/models/[email protected]
/models/[email protected]_5mCG@v2
/models/[email protected]
/models/[email protected]_5mCG@v2
/models/[email protected]
/models/[email protected]_5mCG@v2
/models/[email protected]
/models/[email protected]
/models/[email protected]_5mCG@v0
/models/[email protected]
/models/[email protected]_5mCG@v0
/models/[email protected]
/models/[email protected]_5mCG@v0

To run basecalling follow the normal instructions for running dorado, e.g.:

docker run \
    --gpus 1 \
    -v $PWD:$PWD \
    nanoporetech/dorado \
    dorado basecaller "/models/[email protected]" $PWD/fast5/ \
> output.sam

⁠License

Dorado is distributed under the Oxford Nanopore Technologies PLC. Public License Version 1.0, a copy of which can be found in the source repository⁠.