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RUbioSeq+

M.Rubio

The increasing demand of next-generation sequencing (NGS) studies has remarked the necessity of integrated and reliable pipelines to analyse deep-sequencing experiments in an efficient way. This issue is especially relevant in hospitals and research institutes where regular analyses claim for intuitive and automated workflows to accelerate the delivery of final results minimizing human technical error and ensuring the reproducibility of the technical protocols employed.

We present RUbioSeq+, a stand-alone and multiplatform application for the integrated analysis of NGS data. More specifically, our software implements pipelines for the analysis of single nucleotide and copy-number variation, bisulfite-seq and ChIP-seq experiments using well-established tools to perform these common tasks. RUbioSeq+ is free and includes all the core functionalities implemented in the original release of RUbioSeq (1) but, also, outperforms and expands RUbioSeq capabilities supporting the parallelized analysis of full genomes in computing farms. Moreover, we have included two novel pipelines for ChIPseq analysis. These new workflows covers sample quality control, reads alignment, assessment of biological replicates and peak calling for the detection of both histone marks and transcription factors binding sites. RUbioSeq+ also incorporates a new GUI designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together. Thus, the GUI supports two types of profiles: a) a basic user profile where users with limited skills in bioinformatics can execute all the NGS analysis tasks provided by the software and b) an administration mode where bioinformaticians and advanced users can manage and configure all the technical parameters of the application.

In order to include future improvements, the software has been designed in a modular structure to permit easy adaptation and extension. Reliability of the program has been already proved through experimental assays which have validated the supplied variants. This workflow has been established by the Bioinformatics Unit at CNIO to perform their variant calling analyses.

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