PluMA: Plugin-Based Microbiome Analysis

People


Principal investigator: Prof. Giri Narasimhan

Pipeline architect: Dr. Trevor Cickovski


 

Abstract


Our goal with PluMA is to facilitate the construction of flexible and lightweight analysis pipelines through which a developer can implement a new algorithm in their programming language of choice, and easily test and debug within a larger pipeline alongside stages in different languages that potentially use different file formats.

PluMA accomplishes this through plugins, and has a large collection available in its plugin pool, implemented in various programming languages for both the CPU and GPU. Plugins can be run sequentially to form a pipeline, and can be easily added, removed or substituted through our user interface. Since plugins are dynamically loaded, you can assemble a pipeline by downloading PluMA and only the plugins that you need from the pool.

Note: Our software should not be confused with the PluMa Plugin Management system, and we have no connections or competing interests with PluMa.
Note: PluMA is now a part of OMICTools! Visit their site for details.


 

Citations


Cickovski, T., Narasimhan, G. (2018). Constructing Lightweight and Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA), In press for Bioinformatics, 2018. Abstract available here.

Cickovski, T., Aguiar-Pulido, V., Huang, W., Mahmud, S., Narasimhan, G. (2016). Lightweight Microbiome Analysis Pipelines, In Proceedings of International Work Conference on Bioinformatics and Biomedical Engineering (IWBBIO'16)

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