Canu

Introduction

Canu is a single molecule sequence assembler for genomes large and small.

Detailed usage can be found here: https://github.com/marbl/canu

Versions

• 2.1.1

• 2.2

Commands

• canu

Module

You can load the modules by:

module load biocontainers
module load canu/2.2

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run canu on our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=canu
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers canu/2.2

canu -p Cm -d clavibacter_pacbio genomeSize=3.4m  -pacbio *.fastq