One of the important challenges in analyzing microbiome data is to create flexible lightweight pipelines using a variety of heterogeneous software tools for pipeline stages. These tools can be constructed by third parties using their choice of both language and user interaction, complicating integration of these tools. Here we use the concept of Plugins to build a lightweight pipeline that can accommodate and integrate these heterogeneous tools, independent of these choices. We validate the framework by integrating tools applied at different stages of the microbiome analysis pipeline, implemented in both scripting and compiled languages for both the CPU and GPU.
Cickovski, T., Aguiar-Pulido, V., Huang, W., Mahmud, S., Narasimhan, G. (2016). Lightweight Microbiome Analysis Pipelines, Accepted at IWBBIO