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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===Serial=== | ===Serial=== | ||
* {{#var:app}} | * {{#var:app}} | ||
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* gcc/5.2.0 | * gcc/5.2.0 | ||
<!-- | <!-- | ||
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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 | ||
| + | |||
|}} | |}} | ||
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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).] | |
|}} | |}} | ||
Revision as of 15:53, 19 June 2017
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).
Required Modules
Serial
- canu
- gcc/5.2.0
System Variables
- HPC_{{#uppercase:canu}}_DIR - installation 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: