Difference between revisions of "Genmap"

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==System Variables==
 
==System Variables==
 
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
* 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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<!--Performance-->
 
<!--Performance-->
 
{{#if: {{#var: testing}}|==Performance==
 
{{#if: {{#var: testing}}|==Performance==
 +
 +
|}}
  
 
<!--Faq-->
 
<!--Faq-->
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*'''Q:''' **'''A:'''|}}
 
*'''Q:''' **'''A:'''|}}
 
<!--Citation-->
 
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
+
{{#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:
  
If you use this pipeline and or the companion R package please cite:
 
 
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
 
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