Nextpresso: Next Generation Sequencing Expression Analysis Pipeline

Title:Nextpresso: Next Generation Sequencing Expression Analysis Pipeline

Volume: 13 Issue: 6

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

Affiliation:

• Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO). 3rd Melchor Fernandez Almagro St. 28029, Madrid,Spain

Keywords: RNA-seq, next generation sequencing, transcriptomics, workflow, pipeline, spike-in controls, concurrent processing.

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.

Cite this article as:

Graña O.*, Rubio-Camarillo M. , Fdez-Riverola F. , Pisano D.G. and Glez-Peña D. , Nextpresso: Next Generation Sequencing Expression Analysis Pipeline, Current Bioinformatics 2018; 13 (6) . https://dx.doi.org/10.2174/1574893612666170810153850