Nextpresso: Next Generation Sequencing Expression Analysis Pipeline | BenthamScience

Nextpresso: Next Generation Sequencing Expression Analysis Pipeline

(E-pub Ahead of Print)

Author(s): Osvaldo Graña*, M. Rubio-Camarillo, F. Fdez-Riverola, D. G. Pisano, D. Glez-Peña.

Journal Name: Current Bioinformatics

Abstract:

Background: Many bioinformatics pipelines are available nowadays to analyze transcriptomics data produced by high-throughput RNA sequencing. They implement different workflows that address several analysis tasks, supported by the use of third party programs. Nevertheless, a proper workflow definition for RNA-seq data analysis is still lacking. Objective: To proper define what a comprehensive RNA-seq data analysis workflow should be. Compare all available pipelines and, if such a solution is not available, implement a new pipeline. Method: We have developed a new pipeline integrating state-of-the art programs for different parts of the RNA-seq analysis. We also have used RUbioSeq libraries to achieve a scalable solution. Results: We have defined a comprehensive RNA-seq data analysis workflow, comprising the most common needs demanded by biologists and implemented it in a new pipeline, nextpresso. We also validate it in two case studies presented here. Conclusion: Nexpresso is a new, freely available, pipeline covering the most common needs of RNA-seq data analysis. It is easy to configure, generates user friendly results and scales well for larger studies comprising a high number of samples.

Keywords: RNA-seq, NGS, transcriptomics, gene expression, pipeline, spike-in controls, parallelized execution

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(E-pub Ahead of Print)
DOI: 10.2174/1574893612666170810153850
Price: $95

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