Constructing lightweight and flexible pipelines using Plugin-Based Microbiome Analysis (PluMA)
Abstract
Software pipelines have become almost standardized tools for microbiome analysis. Currently many pipelines are available, often sharing some of the same algorithms as stages. This is largely because each pipeline has its own source language and file formats, making it typically more economical to reinvent the wheel than to learn and interface to an existing package. We present Plugin-Based Microbiome Analysis (PluMA), which addresses this problem by providing a lightweight back end that can be infinitely extended using dynamically loaded plugin extensions. These can be written in one of many compiled or scripting languages. With PluMA and its online plugin pool, algorithm designers can easily plug-and-play existing pipeline stages with no knowledge of their underlying implementation, allowing them to efficiently test a new algorithm alongside these stages or combine them in a new and creative way.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Mar 29, 2018
- Source ID
- 10.1093/bioinformatics/bty198
Entities
People
- Giri Narasimhan
- Trevor Cickovski
Organizations
- Army Research Office
- Eckerd College
- Florida Department of Health
- Florida International University
- Istituto Superiore di SanitÃ
- National Institute of Justice
- National Institutes of Health
- Nvidia
- United States Department of Defense