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RUbioSeq

Alternative name: RUbioSeq+

Allows integrated analysis of next-generation sequencing (NGS) data. RUbioSeq is a multi-platform application that uses well established tools to implement pipelines for DNA-seq, CNAseq, bisulfite-seq and ChIP-seq experiments. The software incorporates a graphical user interface (GUI), designed for interdisciplinary research groups where bioinformaticians and biomedical researchers work together. The modular structure permits easy adaptation and extension.

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RUbioSeq classification

RUbioSeq specifications

Software type:
Pipeline/Workflow
Restrictions to use:
None
Output data:
SAM/BAM, bed, wig, VCF
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
3.8.1
Maintained:
Yes
Interface:
Command line interface, Graphical user interface
Input format:
FASTQ, CSFASTA, QUAL, BAM
Biological technology:
Illumina, Life Technologies
Programming languages:
Perl
Computer skills:
Advanced
Stability:
Stable
Wikipedia:
https://sourceforge.net/p/rubioseq/wiki/RUbioSeq+/

RUbioSeq distribution

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RUbioSeq support

Documentation

Maintainers

  • Miriam Rubio-Camarillo <>
  • Hugo López-Fernández <>

Additional information

http://rubioseq.bioinfo.cnio.es/sites/default/files/PDF/RUbioSeq-book.pdf

Credits

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Publications

Institution(s)

Bioinformatics Unit (UBio), Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Higher Technical School of Computer Engineering, University of Vigo, Ourense, Spain; Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain; Spanish National Bioinformatics Institute (INB), INB Node 2, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

Funding source(s)

Supported by the BLUEPRINT Consortium (FP7/ 2007–2013) under grant agreement number 282510, grant PRB2 (IPT13/0001 - ISCIIISGEFI/ FEDER), a postdoctoral fellowship from the Xunta de Galicia, the
European Union Seventh Framework Programme FP7/REGPOT 2012 2013.1 under grant agreement no. 316265 (BIOCAPS), the “Platform of integration of intelligent techniques for analysis of biomedical information” project (TIN2013-47153-C3-3- R) financed by the Spanish Ministry of Economy and Competitiveness and the “Spanish National Youth Guarantee Implementation Plan” (2013/2016) financed by the Spanish Ministry of Economy and Competitiveness.

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