Attention
Following the recent operating system upgrade, software listings and module load commands now reflect the upgraded system. Some examples and notices are still being updated and may contain outdated guidance.
Dorado
Guidance last updated: 22 July 2025
Dorado is a high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads.
Warning
Dorado requires a dependencies not available on CentOS 7. To make it run on stanage the team containerized the installation using Apptainer. As a result, Dorado is only recommended for use on single-node jobs. The container integration has been abstracted via the module system, allowing you to use Dorado as if it were a standard module.
Note: This is an experimental build. Please report any issues to the HPC support team.
Interactive Usage
After connecting to Stanage (see Establishing a SSH connection), start an interactive session with the following command:
srun --pty bash -i
#This will load the Dorado module and make the command available in your path.
module load dorado/1.0.1
# Run Dorado basecaller
dorado basecaller hac pod5s/ > calls.bam
Batch Submission
#!/bin/bash
#SBATCH --nodes=1
#SBATCH --mem=5G
#SBATCH --time=00:30:00
#SBATCH --cpus-per-task=4
#Email notifications to me@somedomain.com
#SBATCH --mail-user=me@somedomain.com
#Email notifications if the job fails
#SBATCH --mail-type=FAIL
#SBATCH --job-name=dorado_test
module load dorado/1.0.1
dorado basecaller hac pod5s/ > calls.bam
Installation Notes
Dorado requires a newer version of GLIBC not available on the CentOS 7, so it is installed using Apptainer. The container definition file and easyconfig can be found here