Difference between revisions of "SMC++"

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[[Category:Software]][[Category:Biology]][[Category:NGS]]
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[[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-->
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<!--Modules-->
 
<!--Modules-->
==Required Modules==
 
 
===Serial===
 
* gcc/5.2.0
 
* {{#var:app}}
 
<!--
 
===Parallel (OpenMP)===
 
* intel
 
* {{#var:app}}
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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<!--Run-->
 
<!--Run-->
 
{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
 
 
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
 
 
|}}
 
|}}
 
<!--Job Scripts-->
 
<!--Job Scripts-->
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<!--Policy-->
 
<!--Policy-->
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
 
 
WRITE USAGE POLICY HERE (Licensing, usage, access).
 
WRITE USAGE POLICY HERE (Licensing, usage, access).
 
 
|}}
 
|}}
 
<!--Performance-->
 
<!--Performance-->
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 
 
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
 
 
|}}
 
|}}
 
<!--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

smcpp website  

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:

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.