title: RUbioSeq+: A multiplatform application that executes parallelized pipelines to analyse next-generation sequencing data.
abstract: 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/.
authors.affiliation: Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
authors.forename: Miriam
authors.initials: M
authors.lastname: Rubio-Camarillo
authors.affiliation: Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain. Electronic address: hlfernandez@uvigo.es.
authors.forename: Hugo
authors.initials: H
authors.lastname: López-Fernández
authors.affiliation: Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
authors.forename: Gonzalo
authors.initials: G
authors.lastname: Gómez-López
authors.affiliation: Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Carro
authors.affiliation: Spanish National Bioinformatics Institute (INB), INB Node 2, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain.
authors.forename: José María
authors.initials: JM
authors.lastname: Fernández
authors.affiliation: Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
authors.forename: Coral Fustero
authors.initials: CF
authors.lastname: Torre
authors.affiliation: Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain.
authors.forename: Florentino
authors.initials: F
authors.lastname: Fdez-Riverola
authors.affiliation: Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain.
authors.forename: Daniel
authors.initials: D
authors.lastname: Glez-Peña
mesh_terms: D047369:Chromatin Immunoprecipitation; D056915:DNA Copy Number Variations; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software; D014584:User-Computer Interface
keywords: Bisulfite-Seq; CNV; ChIPSeq; NGS analysis; Variant calling; Whole-genome