Publications

Miriam Rubio-Camarillo, Hugo López-Fernández, Gonzalo Gómez-López, Ángel Carro, José María Fernández, Coral Fustero Torre, Florentino Fdez-Riverola,Daniel Glez-Peña.

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.

 

 

 

2017, Computer Methods and Programs in Biomedicine, 138

Miriam Rubio-Camarillo1,*,Gonzalo Gómez-López2, José M. Fernández3, Alfonso Valencia1,3 and David G. Pisano2

1Structural Computational Biology Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain

2Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain 

3Spanish National Bioinformatics Institute (INB), INB Node 2, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain

RUbioSeq has been developed to facilitate the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (single-nucleotide variants and copy number variations) and to perform bisulfite-seq analyses automatically. RUbioSeq’s variant analysis results have been already validated and published.

2013, Bioinformatics, 29 (13): 1687-1689

Citations

NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation.
Verónica García-Carpizo et al.
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.
Federico Abascal et al.
The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues
Ana Cuadrado et al.
Methodological aspects of whole-genome bisulfite sequencing analysis
Swarnaseetha Adusumalli et al.
Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses
Xiaoyi Gao et al.
Node-Oriented Workflow (NOW): A Command Template Workflow Management Tool for High Throughput Data Analysis Pipelines
Eric B. Lipsky et al.
Functional and molecular characterization of inherited platelet disorders in the Iberian Peninsula: results from a collaborative study
Sánchez-Guiu I et al.
Molecular Diagnostics and Treatment of Pancreatic Cancer Systems and Network Biology Approaches: Bioinformatics analysis of pancreas cancer genome in high-throughput genomic Technologies
Enrique Carrillo-de Santa Pau et al.
New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing
Elena Doménech et al.
CSF3R T618I co-occurs with mutations of splicing and epigenetic genes and with a new PIM3 truncated fusion gene in chronic neutrophilic leukemia
J Menezes et al.

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