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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.

Canu

Canu is a single-molecule sequence assembler for genomes large and small. It is designed for high-noise long reads such as those from PacBio or Oxford Nanopore sequencers, and performs correction, trimming and assembly.

License

Free to use and open source under GNU GPLv2.

Available

  • Roihu: 2.2, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load canu/2.2

A basic assembly specifies a prefix (-p), an output directory (-d), the genome size and the read type:

canu -p asm -d assembly genomeSize=5m -nanopore reads.fq.gz

Grid (Slurm) submission

By default Canu detects the Slurm batch system and submits its own jobs to the queue. To instead run the whole assembly inside a single batch job allocation, set useGrid=false (recommended for small and medium genomes). For large genomes you can let Canu use the grid and pass account/partition settings with gridOptions="--account=<project> --partition=small".

Example batch script

#!/bin/bash
#SBATCH --job-name=canu
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load canu/2.2

canu -p asm -d assembly genomeSize=5m -nanopore reads.fq.gz \
    useGrid=false maxThreads=$SLURM_CPUS_PER_TASK

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information