Difference between revisions of "SMC++"
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(Created page with "Category:SoftwareCategory:BiologyCategory:NGS {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|smcpp}} |{{#vardefine:url|https://github.com/popgenmethods/smcpp}}...") |
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Genomics]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|smcpp}} | |{{#vardefine:app|smcpp}} | ||
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
|{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | ||
| − | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | + | |{{#vardefine:job|1}} <!--JOB 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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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY | WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY | ||
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|}} | |}} | ||
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<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
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WRITE USAGE POLICY HERE (Licensing, usage, access). | WRITE USAGE POLICY HERE (Licensing, usage, access). | ||
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|}} | |}} | ||
<!--Performance--> | <!--Performance--> | ||
{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE | WRITE_PERFORMANCE_TESTING_RESULTS_HERE | ||
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|}} | |}} | ||
<!--Faq--> | <!--Faq--> | ||
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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://www.nature.com/ng/journal/v49/n2/abs/ng.3748.html J. Terhorst, J. A. Kamm, and Y. S. Song. Robust and scalable inference | + | [http://www.nature.com/ng/journal/v49/n2/abs/ng.3748.html J. Terhorst, J. A. Kamm, and Y. S. Song. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics, 49(2):303–309, 2017.] |
| − | of population history from hundreds of unphased whole genomes. Nature | ||
| − | Genetics, 49(2):303–309, 2017.] | ||
|}} | |}} | ||
Latest revision as of 23:52, 21 August 2022
Description
SMC++ is a program for estimating the size history of populations from whole genome sequence data.
System Variables
- HPC_SMCPP_DIR - installation directory
- HPC_SMCPP_BIN - executable directory
Job Script Examples
See the SMC++_Job_Scripts page for smcpp Job script examples.
Citation
If you publish research that uses smcpp you have to cite it as follows: