Difference between revisions of "Canu"

Latest revision as of 14:26, 14 April 2020

Description

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

Environment Modules

Run module spider canu to find out what environment modules are available for this application.

System Variables

HPC_CANU_DIR - installation directory
HPC_CANU_BIN - executable directory
HPC_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

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 for canu parameters.

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).

@@ Line 43: / Line 43: @@
   -maxMemory=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 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.
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