Dorado¶

Dorado is an easy-to-use basecaller for Oxford Nanopore reads. The bundle packages version 0.8.3.

Usage example¶

If the system has a NVIDIA GPU then the following loads the Dorado bundle:

1	`module load dorado`

With the module loaded, Dorado can be run as shown below:

dorado

The pod5 command can be run as shown below:

pod5

The dorado_shell can be used to access a shell in the bundle.

1	`dorado_shell`

If the system does not have NVIDIA GPU then the submit command can be used to submit a GPU job and run dorado commands.

An example script to run Dorado:

#!/bin/bash
dorado basecaller $MODELS_DIR/dna_r10.4.1_e8.2_400bps_sup@v4.3.0 pod5/ \
        --min-qscore 10 --kit-name SQK-NBD114-24 \
        -x "cuda:$CUDA_VISIBLE_DEVICES" > calls.bam

dorado demux --output-dir demux/ --no-classify calls.bam

submit --profile=vnc_gpu --name=dorado_test --gpu=2 --threads=16 \
        --memory=128gb --input='pod5/*' --input=run.sh \
        --output='dorado_output/*' --module=dorado \
        --mkexec=run.sh --command=./run.sh --

Adjust according to your needs.

Performance notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

Community guides and tutorials¶

No community guides available.

Official site and documentation¶

Licensing information¶

Dorado is licensed under the Oxford Nanopore Technologies PLC. Public License Version 1.0
POD5 is licensed under the Mozilla Public License, v2.0

Primary citation¶

External guides and resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za