Difference between revisions of "Genmap"

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(Created page with "Category:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|genmap}} |{{#vardefine:url|REPLACE}} <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> |{{#vardefine...")
 
 
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{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|genmap}}
 
|{{#vardefine:app|genmap}}
|{{#vardefine:url|REPLACE}}
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|{{#vardefine:url|https://github.com/cpockrandt/genmap}}
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
 
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
DESCRIPTION
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Ultra-fast Computation of Genome Mappability (GenMap) computes the uniqueness of k-mers for each
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position in the genome while allowing for upto e mismatches.
  
 
<!--Modules-->
 
<!--Modules-->
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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation 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
 
  
 
|}}
 
|}}
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<!--Policy-->
 
<!--Policy-->
 
{{#if: {{#var: policy}}|==Usage Policy==
 
{{#if: {{#var: policy}}|==Usage Policy==
 
WRITE USAGE POLICY HERE (Licensing, usage, access).
 
  
 
|}}
 
|}}
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{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
  
WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
  
|}}
 
 
<!--Faq-->
 
<!--Faq-->
 
{{#if: {{#var: faq}}|==FAQ==
 
{{#if: {{#var: faq}}|==FAQ==
 
*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
<!--Citation-->
 
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
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{{#if: {{#var: citation}}1|==Citation==
 
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:
  
WRITE_CITATION_HERE
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Reginato M. 2022. A pipeline for assembling low-copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 10:e14525 https://doi.org/10.7717/peerj.14525
  
 
|}}
 
|}}

Latest revision as of 21:20, 17 May 2023

Description

genmap website  

Ultra-fast Computation of Genome Mappability (GenMap) computes the uniqueness of k-mers for each position in the genome while allowing for upto e mismatches.

Environment Modules

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

System Variables

  • HPC_GENMAP_DIR - installation directory
  • HPC_GENMAP_BIN - executable directory




Citation

If you publish research that uses genmap you have to cite it as follows:

Reginato M. 2022. A pipeline for assembling low-copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 10:e14525 https://doi.org/10.7717/peerj.14525