Difference between revisions of "Pyani"
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(Created page with "Category:SoftwareCategory:biologyCategory:genomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|pyani}} |{{#vardefine:url|https://github.com/widdowquinn/pyan...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Phylogenetics]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|pyani}} | |{{#vardefine:app|pyani}} | ||
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|{{#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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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: testing}}|==Performance== | {{#if: {{#var: testing}}|==Performance== | ||
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|}} | |}} | ||
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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: | ||
| − | + | https://github.com/widdowquinn/pyani/blob/master/CITATIONS | |
|}} | |}} | ||
Latest revision as of 19:44, 21 August 2022
Description
pyani is a Python3 module that provides support for calculating average nucleotide identity (ANI) and related measures for whole genome comparisons, and rendering relevant graphical summary output. Where available, it takes advantage of multicore systems, and can integrate with SGE/OGE-type job schedulers for the sequence comparisons.
Environment Modules
Run module spider pyani to find out what environment modules are available for this application.
System Variables
- HPC_PYANI_DIR - installation directory
- HPC_PYANI_BIN - executable directory
Citation
If you publish research that uses pyani you have to cite it as follows:
https://github.com/widdowquinn/pyani/blob/master/CITATIONS