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Comput Methods Programs Biomed. 2017 Jan;138:73-81. doi: 10.1016/j.cmpb.2016.10.008. Epub 2016 Oct 26.

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

Author information

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/.

KEYWORDS:

Bisulfite-Seq; CNV; ChIPSeq; NGS analysis; Variant calling; Whole-genome

PMID:
27886717
DOI:
10.1016/j.cmpb.2016.10.008
[Indexed for MEDLINE]
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