RUbioSeq pipeline

RUbioSeq specifications

Information


Unique identifier OMICS_00072
Name RUbioSeq
Alternative name RUbioSeq+
Software type Pipeline/Workflow
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format FASTQ, CSFASTA, QUAL, BAM
Output data SAM/BAM, bed, wig, VCF
Biological technology Illumina, Life Technologies
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.8.1
Stability Stable
Maintained Yes
Wikipedia https://sourceforge.net/p/rubioseq/wiki/RUbioSeq+/

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Documentation


Maintainers


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

Additional information


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

Publications for RUbioSeq

RUbioSeq IN pipeline

2015
PMCID: 4381060
PMID: 25735743
DOI: 10.1093/nar/gkv144

[…] using macs v1.4 setting a p-value cut-off of 10−5 and fdr threshold better than 5% (50). all comparisons were done with the input track as control and each one of the data sets as treatment, using rubioseq 2.0 as automation analysis pipeline (51). genomic interval overlaps and signal distributions were obtained using bedtools v2.12 (52), peakanalyzer v1.3 (53) and custom unix shell scripting. […]

RUbioSeq 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
RUbioSeq 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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