RUbioSeq protocols

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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 pipelines

 (2)
2016
PMCID: 5015087
PMID: 27604143
DOI: 10.1038/srep32952

[…] calculated using bamtogff (https://github.com/bradnercomputation/pipeline/blob/master/bamtogff.py). for visualization of the changes in h3k36me2 levels bam files with aligned reads generated using rubioseq3.7 were converted to sorted bed files. reads per nucleotide were counted for each sample with bedtools 2.23.0 and divided by the total number of reads in the sample. reads counts […]

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% (). 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 (). genomic interval overlaps and signal distributions were obtained using bedtools v2.12 (), peakanalyzer v1.3 () and custom unix shell scripting. […]


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RUbioSeq in publications

 (5)
PMCID: 5155386
PMID: 27964752
DOI: 10.1186/s13059-016-1090-1

[…] a phylogenetic tree for all these ervs using the bionj method [] (additional file : section 15)., to identify and polarize substitutions in eurasian and iberian lynxes we called variants with the rubioseq pipeline [] using the genome of domestic cat (version 6.2, felcat5) as reference (additional file : section 16). based on the genotype of each lynx species, we selected all those sites, […]

PMCID: 5015087
PMID: 27604143
DOI: 10.1038/srep32952

[…] calculated using bamtogff (https://github.com/bradnercomputation/pipeline/blob/master/bamtogff.py). for visualization of the changes in h3k36me2 levels bam files with aligned reads generated using rubioseq3.7 were converted to sorted bed files. reads per nucleotide were counted for each sample with bedtools 2.23.0 and divided by the total number of reads in the sample. reads counts […]

PMCID: 4598567
PMID: 26403419
DOI: 10.1038/ncomms9383

[…] were paired-end sequenced on an illumina genome analyzer ii sequencing platform, using two lanes per sample and generating 78-bp-long reads. filtering of reads and variant calling were done with the rubioseq software suite of parallelized pipelines. pcr duplicates, overrepresented sequences and low quality reads were filtered with a modular set of analyses considering per base and per sequence […]

PMCID: 3880437
PMID: 24212482
DOI: 10.1038/bcj.2013.54

[…] (agilent) covering 50 mb of coding exons (∼1.60% of the genome). after massive parallel sequencing using the genome analyzer iix (illumina), candidate somatic mutations were identified using rubioseq software. the bioinformatics analysis and the filtering steps to identify the coding variants are detailed in the ., after discarding the variants present in the matched normal dna […]

PMCID: 3880438
PMID: 24212483
DOI: 10.1038/bcj.2013.55

[…] of the genes involved in the pathogenesis of cnl, wes was performed on matched tumor and oral mucosa cell (germline) samples from the patient. candidate somatic mutations were identified using rubioseq software. the bioinformatics analysis and the filtering steps to identify the coding variants are detailed in the . in total, we found 1437 candidate variants; among them, 797 were somatic […]


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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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