Canu

Description

canu website  

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

Required Modules

Serial

• canu
• gcc/5.2.0

System Variables

• HPC_{{#uppercase:canu}}_DIR - installation directory
• HPC_{{#uppercase:canu}}_BIN - executable directory
• HPC_{{#uppercase:canu}}_DOC - documentation directory

Additional Information

When running Canu you should specify Memory and CPU usage in your command. e.g.

#SBATCH --cpus-per-task=8 
#SBATCH --mem=10g

-maxThreads=8
-maxMemory=10g

Citation

If you publish research that uses canu you have to cite it as follows:

Koren S, Walenz BP, Berlin K, Miller JR, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research. (2017).