Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
module spider canu to find out what environment modules are available for this application.
- HPC_CANU_DIR - installation directory
- HPC_CANU_BIN - executable directory
- HPC_CANU_DOC - documentation directory
When running Canu you should specify Memory and CPU usage in your command. e.g.
#SBATCH --cpus-per-task=8 #SBATCH --mem=10g
If your canu jobs run out of memory make sure to set scheduled job resources in gridOptions and merylMemory respectively to make sure meryl does not exceed the requested memory. [See https://canu.readthedocs.io/en/latest/parameter-reference.html https://canu.readthedocs.io/en/latest/parameter-reference.html] for canu parameters.
If you publish research that uses canu you have to cite it as follows: