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

Canu is a hierachical assembly pipeline which runs in four steps:

  • Detect overlaps in high-noise sequences using MHAP
  • Generate corrected sequence consensus
  • Trim corrected sequences
  • Assemble trimmed corrected sequences


Version on CSC's Servers

Taito: 1.6, 1.7, 1.8


To load Canu:

module load java/oracle/1.8
module load canu

To see full list of options:

canu -options

Canu will split your assembly job to many smaller subjobs and will then submit these subjobs to the queue system. That means that Canu front-end program does not need to be run as a batch job. It can be run simply from the command line.


These commands will run the example E. coli assembly as described in the Canu Quick Start guide.

First load the sample data:

curl -L -o p6.25x.fastq

Then run Canu:

canu -p ecoli -d ecoli-auto genomeSize=4.8m -pacbio-raw p6.25x.fastq "gridOptions=-t 72:00:00" maxMemory=32 maxThreads=4

With this command Canu will correct the reads, then trim the reads and then assemble the reads to unitigs. You'll notice the Canu front-end program will submit the subjobs, print some information and exit. This will be quite fast. You can then use the squeue and sacct commands to check the progress of the subjobs (See Taito User Guide for more details on these commands).

squeue -u <username>




Berlin K, Koren S, Chin CS, Drake PJ, Landolin JM, Phillippy AM Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing. Nature Biotechnology. (2015).



The developers provide a quick start guide and a more detailed tutorial.