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Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

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Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies.

Shanrong Zhao¹, Kurt Prenger², Lance Smith³

¹Systems Pharmacology and Biomarkers, Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, CA 92121, USA.

ISRN Bioinformatics

|May 5, 2015

Summary

This summary is machine-generated.

Stormbow is a new cloud-based tool for analyzing large RNA-Seq datasets. It offers a scalable and cost-effective solution for transcriptome profiling and differential gene expression studies.

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Area of Science:

Genomics
Bioinformatics

Background:

RNA-sequencing (RNA-Seq) is increasingly replacing microarrays for transcriptome profiling.
Decreasing sequencing costs have led to a rapid increase in RNA-Seq dataset size and number.
Analyzing large-scale RNA-Seq data locally presents significant computational challenges.

Purpose of the Study:

To develop a scalable, cost-effective cloud-based software package for processing large volumes of RNA-Seq data.
To address the practical challenges of analyzing massive RNA-Seq datasets.

Main Methods:

Development of Stormbow, a cloud-based software package for parallel RNA-Seq data processing.
Utilizing Amazon Web Services for scalable computational resources.
Testing Stormbow's performance on 178 RNA-Seq samples.

Main Results:

Stormbow processed an average of 100 million reads per RNA-Seq sample in 6-8 hours.
The average cost per sample was $3.50.
The tool demonstrated scalability for handling large datasets.

Conclusions:

Stormbow is a scalable, cost-effective, and open-source tool for large-scale RNA-Seq data analysis.
The software is readily available for processing Illumina RNA-Seq datasets.
Cloud-based analysis offers a practical solution for big data challenges in transcriptomics.