Canu

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

• Version: 1.8
• Added: September, 2017
• Updated: October, 2018
• Link: http://canu.readthedocs.io/

See which versions of canu are available:

$ module avail canu

Load one version into your environment and run it:

$ module load canu/1.8
$ canu

Note: By default canu will try to use all the CPUs available on the machine so you should limit it to the number of CPUs requested in your SLURM jobs with the maxThreads option. See the documentation.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/marbl/canu/releases/download/v1.8/canu-1.8.Linux-amd64.tar.xz
$ tar xf canu-1.8.Linux-amd64.tar.xz
$ sudo mkdir -p /export/apps/canu/1.8
$ sudo cp -r canu-1.8/* /export/apps/canu/1.8