RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data

Abstract

This is the peer reviewed version of the following article: Computer Methods and Programs in Biomedine 138 (2016): 73-81, which has been published in final form at http://dx.doi.org/10.1016/j.cmpb.2016.10.008Background and objective To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines. Methods We have selected well-established software to construct a suite of automated and parallelized workflows to analyse NGS data for DNA-seq (single-nucleotide variants (SNVs) and indels), CNA-seq, bisulfite-seq and ChIP-seq experiments. Results Here, we present RUbioSeq+, an updated and extended version of RUbioSeq, a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data. This new version includes: (i) an interactive graphical user interface (GUI) that facilitates its use by both biomedical researchers and bioinformaticians, (ii) a new pipeline for ChIP-seq experiments, (iii) pair-wise comparisons (case–control analyses) for DNA-seq experiments, (iv) and improvements in the parallelized and multithreaded execution options. Results generated by our software have been experimentally validated and accepted for publication. Conclusions RUbioSeq+ is free and open to all users at http://rubioseq.bioinfo.cnio.es/.M.R-C is funded by the BLUEPRINT Consortium (FP7/ 2007-2013) under grant agreement number 282510. J.M.F is funded by the INB Node 2 - CNIO, a member of Proteored - PRB2-ISCIII and is supported by grant PT13/0001, of the PE I+D+i 2013-2016, funded by ISCIII and FEDER. H.L-F is funded by a postdoctoral fellowship from the Xunta de Galicia. F.F-R and D.G-P are funded by the European Union's Seventh Framework Programme FP7/REGPOT 2012 2013.1 under grant agreement n° 316265 (BIOCAPS) and the "Platform of integration of intelligent techniques for analysis of biomedical information" project (TIN2013-47153-C3-3-R) financed by the Spanish Ministry of Economy and Competitiveness C.FT is funded by the "Spanish National Youth Guarantee Implementation Plan” (2013/2016) financed by the Spanish Ministry of Economy and Competitivenes