Attention
Advance Notice: Bessemer will be retired at the end of the day on Friday 31st October 2025.
Dorado
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