Software: Canu
Description
Canu is a single molecule sequence assembler for genomes large and small.
Available Versions
Unspecified: | 2.1.1 2.2 |
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Detailed usage can be found here: https://github.com/marbl/canu
Commands
- canu
Module
You can load the modules by:
module load biocontainers
module load canu/2.2
Example job
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