Difference between revisions of "Imoka"
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(Created page with "Category:SoftwareCategory:BiologyGenomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|imoka}} |{{#vardefine:url|https://github.com/RitchieLabIGH/iMOKA/tree/...") |
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| − | [[Category: | + | [[Category:biology]] |
| + | [[Category:genomics]] | ||
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|imoka}} | |{{#vardefine:app|imoka}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#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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{{#if: {{#var: url}}| | {{#if: {{#var: url}}| | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| + | iMOKA is a software that enables a comprehensive analysis of sequencing data | ||
| + | from large cohorts to generate robust classification models or explore | ||
| + | specific genetic elements associated with disease etiology. iMOKA uses a fast | ||
| + | and accurate feature reduction step that combines a Naïve Bayes Classifier | ||
| + | augmented by an adaptive Entropy filter and a graph-based filter to rapidly | ||
| + | reduce the search space. By using a flexible file format and distributed | ||
| + | indexing, iMOKA can easily integrate data from multiple experiments and also | ||
| + | reduces disk space requirements. | ||
| − | |||
| − | |||
| − | |||
<!--Modules--> | <!--Modules--> | ||
| Line 26: | Line 32: | ||
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_IMOKA_DIR - installation directory |
| + | * HPC_IMOKA_BIN - executable directory | ||
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 33: | Line 40: | ||
<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | Commands exposed from the container: | |
| − | + | * iMOKA_core | |
| − | + | * preprocess.sh | |
| + | * gmap | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
| Line 60: | Line 68: | ||
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: | ||
| − | + | Lorenzi, C., Barriere, S., Villemin, J. et al. iMOKA: k-mer based software to analyze large collections of sequencing data. Genome Biol 21, 261 (2020). https://doi.org/10.1186/s13059-020-02165-2 | |
|}} | |}} | ||
Latest revision as of 17:07, 27 May 2022
Description
imoka website
iMOKA is a software that enables a comprehensive analysis of sequencing data
from large cohorts to generate robust classification models or explore
specific genetic elements associated with disease etiology. iMOKA uses a fast
and accurate feature reduction step that combines a Naïve Bayes Classifier
augmented by an adaptive Entropy filter and a graph-based filter to rapidly
reduce the search space. By using a flexible file format and distributed
indexing, iMOKA can easily integrate data from multiple experiments and also
reduces disk space requirements.
Environment Modules
Run module spider imoka to find out what environment modules are available for this application.
System Variables
- HPC_IMOKA_DIR - installation directory
- HPC_IMOKA_BIN - executable directory
Additional Information
Commands exposed from the container:
- iMOKA_core
- preprocess.sh
- gmap
Citation
If you publish research that uses imoka you have to cite it as follows:
Lorenzi, C., Barriere, S., Villemin, J. et al. iMOKA: k-mer based software to analyze large collections of sequencing data. Genome Biol 21, 261 (2020). https://doi.org/10.1186/s13059-020-02165-2