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Protocols

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+/

Download


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Versioning


No version available

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 citations

 (6)
call_split

Molecular basis of targeted therapy in T/NK cell lymphoma/leukemia: A comprehensive genomic and immunohistochemical analysis of a panel of 33 cell lines

2017
PLoS One
PMCID: 5432176
PMID: 28505169
DOI: 10.1371/journal.pone.0177524
call_split See protocol

[…] ing the Illumina TruSeq Custom Amplicon Kit v1.5 and sequenced on a MiSeq sequencer (Illumina, San Diego, CA), following the manufacturer’s instructions. Variants were called using MiSeq Reporter and RUbioSeq [], employing the default settings, and were visually inspected on IGV (www.broadinstitute.org/igv/). Variants were annotated with Variant Effect Predictor (GRCh37, http://grch37.ensembl.org/ […]

library_books

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

2016
Genome Biol
PMCID: 5155386
PMID: 27964752
DOI: 10.1186/s13059-016-1090-1

[…] 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, eithe […]

library_books

NSD2 contributes to oncogenic RAS driven transcription in lung cancer cells through long range epigenetic activation

2016
Sci Rep
PMCID: 5015087
PMID: 27604143
DOI: 10.1038/srep32952

[…] re 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 were subtrac […]

call_split

A mutation in the POT1 gene is responsible for cardiac angiosarcoma in TP53 negative Li–Fraumeni like families

2015
Nat Commun
PMCID: 4598567
PMID: 26403419
DOI: 10.1038/ncomms9383
call_split See protocol

[…] 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 qu […]

library_books

The contribution of cohesin SA1 to gene expression and chromatin architecture in two murine tissues

2015
Nucleic Acids Res
PMCID: 4381060
PMID: 25735743
DOI: 10.1093/nar/gkv144

[…] rmed 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. All the […]

library_books

Functional and molecular characterization of inherited platelet disorders in the Iberian Peninsula: results from a collaborative study

2014
Orphanet J Rare Dis
PMCID: 4302577
PMID: 25539746
DOI: 10.1186/s13023-014-0213-6

[…] not confirmed by functional and molecular studies, exome sequencing was performed (Agilent SureSelect Capture v4 + UTRs and Genome Analyzer IIx platform, Agilent Technologies, Santa Clara, CA). Using RUbioSeq software [] sequencing data were aligned to the human reference genome (GRCh37) and exome variant analysis and functional prediction were performed with the default parameters for somatic var […]

Citations

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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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