R-SAP – a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data

Currently available analysis tools are often not easily installed by the general biologist and most of them lack inherent parallel processing capabilities widely recognized as an essential feature of next-generation bioinformatics tools. Presented here is a user-friendly and fully automated RNA-Seq analysis pipeline (R-SAP) with built-in multi-threading capability to analyze and quantitate high-throughput RNA-Seq datasets. R-SAP follows a hierarchical decision making procedure to accurately characterize various classes of transcripts and achieves a near linear decrease in data processing time as a result of increased multi-threading. In addition, RNA expression level estimates obtained using R-SAP display high concordance with levels measured by microarrays.

R-SAP program is publicly available at www.mcdonaldlab.biology.gatech.edu/r-sap.htm.

  • Mittal VK, McDonald JF. (2012) R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acids Res [Epub ahead of print]. [article]