Miriam Rubio-Camarillo1, Hugo López-Fernández2, Gonzalo Gómez-López1, Ángel Carro1, José María Fernández3, Coral Fustero Torre1, Florentino Fdez-Riverola4, Daniel Glez-Peña4. 1. Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. 2. 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. 3. Spanish National Bioinformatics Institute (INB), INB Node 2, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain. 4. Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain.
Abstract
BACKGROUND 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/. Copyright Â
BACKGROUND 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/. Copyright Â
Authors: Rosa María Marión; Juan J Montero; Isabel López de Silanes; Osvaldo Graña-Castro; Paula Martínez; Stefan Schoeftner; José Alejandro Palacios-Fábrega; Maria A Blasco Journal: Elife Date: 2019-08-20 Impact factor: 8.140
Authors: Laia Richart; Eleonora Lapi; Vera Pancaldi; Mirabai Cuenca-Ardura; Enrique Carrillo-de-Santa Pau; Miguel Madrid-Mencía; Hélène Neyret-Kahn; François Radvanyi; Juan Antonio Rodríguez; Yasmina Cuartero; François Serra; François Le Dily; Alfonso Valencia; Marc A Marti-Renom; Francisco X Real Journal: Nucleic Acids Res Date: 2021-11-08 Impact factor: 16.971