Canu

Introduction

Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

For more information, please check:

BioContainers: https://biocontainers.pro/tools/canu

Home page: https://canu.readthedocs.io/en/latest/

Versions

• 2.1.1

• 2.2

Commands

• canu

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 clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=canu
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load canu/XXXX ### you can run *module avail canu* to check all available versions

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