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| | + | |{{#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}}}}|}} | ||
| − | + | 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. | ||
<!--Modules--> | <!--Modules--> | ||
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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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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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|}} | |}} | ||
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<!--Policy--> | <!--Policy--> | ||
{{#if: {{#var: policy}}|==Usage Policy== | {{#if: {{#var: policy}}|==Usage Policy== | ||
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|}} | |}} | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
| − | + | |}} | |
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<!--Faq--> | <!--Faq--> | ||
{{#if: {{#var: faq}}|==FAQ== | {{#if: {{#var: faq}}|==FAQ== | ||
*'''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: | ||
| − | + | 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
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