Submit Manuscript  

Article Details


Nextpresso: Next Generation Sequencing Expression Analysis Pipeline

[ Vol. 13 , Issue. 6 ]

Author(s):

O. Graña*, M. Rubio-Camarillo, F. Fdez-Riverola, D.G. Pisano and D. Glez-Peña   Pages 583 - 591 ( 9 )

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, next generation sequencing, transcriptomics, workflow, pipeline, spike-in controls, concurrent processing.

Affiliation:

Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO). 3rd Melchor Fernandez Almagro St. 28029, Madrid, Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO). 3rd Melchor Fernandez Almagro St. 28029, Madrid, ESEI - Escuela Superior de Ingenieria Informatica, Edificio Politecnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Bioinformatics Unit, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO). 3rd Melchor Fernandez Almagro St. 28029, Madrid, ESEI - Escuela Superior de Ingenieria Informatica, Edificio Politecnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense

Graphical Abstract:



Read Full-Text article