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

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

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.

MeSH terms

  • Chromatin Immunoprecipitation
  • DNA Copy Number Variations
  • High-Throughput Nucleotide Sequencing / methods*
  • Polymorphism, Single Nucleotide
  • Software*
  • User-Computer Interface