Difference between revisions of "Canu"

Revision as of 14:26, 14 April 2020

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

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

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 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:

@@ Line 20: / Line 20: @@
 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
-<!--Modules-->
+==Environment Modules==
-==Required Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-* gcc/5.2.0
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
 * HPC_{{uc:{{#var:app}}}}_DIR - installation directory
@@ Line 55: / 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.
 |}}