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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

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NGSANE: a lightweight production informatics framework for high-throughput data analysis.

Fabian A Buske¹, Hugh J French, Martin A Smith

¹Cancer Epigenetics Program, Cancer Research Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, RNA Biology and Plasticity Laboratory, Garvan Institute of Medical Research, St Vincent's Clinical School, University of NSW, Sydney 2010, Australia and Division of Computational Informatics, CSIRO, Sydney 2113, Australia.

Bioinformatics (Oxford, England)

|January 29, 2014

Summary

This summary is machine-generated.

Next Generation Sequencing ANalysis for Enterprises (NGSANE) is a flexible, Linux-based framework for automating next-generation sequencing data analysis. It uses modular components to overcome rapid technological obsolescence in bioinformatics pipelines.

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Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Next-generation sequencing (NGS) data analysis relies on software pipelines.
Rapid technological advancements and evolving analysis methods frequently render existing pipelines obsolete.
Existing pipelining systems often use rigid program call wrapping, limiting flexibility.

Purpose of the Study:

To present a novel framework for automating NGS data analysis.
To address the challenge of rapidly depreciating software components in bioinformatics pipelines.
To offer a flexible and efficient solution for processing raw sequence data.

Main Methods:

Developed Next Generation Sequencing ANalysis for Enterprises (NGSANE), a Linux-based framework.
Implemented NGSANE using Linux bash commands for modularity and flexibility.
Enabled high-performance computing for efficient data processing.

Main Results:

NGSANE minimizes setup and processing overhead for new projects.
The framework maintains full flexibility for custom scripting.
Modular components allow for easier updates and adaptation to evolving technologies.

Conclusions:

NGSANE provides a robust and adaptable solution for NGS data analysis.
The Linux bash implementation facilitates the use of hot-swappable modular components.
This framework enhances the longevity and efficiency of bioinformatics informatics pipelines.