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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

Dorado

Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. On Roihu it is provided as a GPU-accelerated build for the GH200 GPU nodes.

License

Dorado is distributed under the Oxford Nanopore Technologies PLC Public License v1.0. The license permits use solely for research purposes, defined as internal research not intended for or directed towards commercial advantage or monetary compensation. Sponsored or grant-funded research is permitted under the license.

Available

  • Roihu-GPU: 2.1.1, via the bio-apps module (GPU nodes only).

Dorado runs on the Roihu GPU (GH200) nodes. Log in to roihu-gpu.csc.fi and load the modules there so you get the GPU build.

Usage

Dorado is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the Dorado module:

module load bio-apps/v202603
module load dorado/2.1.1

Dorado uses basecalling models that are downloaded on first use. Download them to a writable location (for example your project's /scratch), or let dorado basecaller fetch the model automatically when run from a writable working directory:

dorado download --model dna_r10.4.1_e8.2_400bps_sup@v5.0.0

Example batch script

Dorado must run on a GPU node. Below is a sample GPU batch job:

#!/bin/bash
#SBATCH --job-name=dorado
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=gpumedium
#SBATCH --time=08:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --gres=gpu:gh200:1

module load bio-apps/v202603
module load dorado/2.1.1

dorado basecaller sup pod5_dir/ > calls.bam

Replace <project> with your CSC project (for example project_2001234). The sup argument selects the super-accuracy model; dorado downloads it if it is not already present.

See creating a batch job script for Roihu for more information about running batch jobs, and the GPU partitions for available GPU resources.

Support

CSC Service Desk

More information