Difference between revisions of "Canu"
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). | 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 <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
| + | * HPC_{{uc:{{#var:app}}}}_DOC - documentation directory | ||
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<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 https://canu.readthedocs.io/en/latest/parameter-reference.html] for canu parameters. | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
| − | + | [http://genome.cshlp.org/content/27/5/722 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).] | |
|}} | |}} | ||
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: