Nextpresso: Next Generation Sequencing Expression Analysis Pipeline

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

Journal Name: Current Bioinformatics

Volume 13 , Issue 6 , 2018

Graphical Abstract:


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.

Rights & PermissionsPrintExport Cite as

Article Details

VOLUME: 13
ISSUE: 6
Year: 2018
Page: [583 - 591]
Pages: 9
DOI: 10.2174/1574893612666170810153850
Price: $58

Article Metrics

PDF: 2