Oqtans statistics

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Read alignment Normalization Differential expression De novo transcriptome assembly Bioinformatics workflows Novel transcript quantification Reference-based transcriptome assembly Spliced read alignment

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Oqtans specifications

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Information

Unique identifier	OMICS_01407
Name	Oqtans
Alternative name	Online quantitative transcriptome analysis
Software type	Pipeline/Workflow
Interface	Command line interface
Restrictions to use	None
Biological technology	Illumina
Operating system	Unix/Linux, Mac OS
Programming languages	C, C++, Java, MATLAB, Perl, Python, R
License	GNU General Public License version 2.0
Computer skills	Advanced
Stability	Stable
Maintained	Yes

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Maintainers

Gunr Rätsch <>
Vipin Sreedharan <>

Publication for Online quantitative transcriptome analysis

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

2014 Bioinformatics

PMCID: 3998122

PMID: 24413671

DOI: 10.1093/bioinformatics/btt731

Oqtans in publications

(2)

Scalability and Validation of Big Data Bioinformatics Software

PMCID: 5537105

PMID: 28794828

DOI: 10.1016/j.csbj.2017.07.002

[…] there have been many bioinformatics saas solutions to perform tasks ranging from short-read alignment (cloudaligner and sparkbwa ), variant calling (halvade and churchill ) and rna-seq analysis (oqtans and falco ). in platform as a service, users are provided with a platform for developing their own software. some paas providers also provide support for automatically scaling the computing […]

Highlights from the ISCB Student Council Symposium 2013

PMCID: 4079984

PMID: 25077567

DOI: 10.1186/1471-2105-15-S3-A1

[…] previous tuberculosis loci, and to introduce novel genes and sub-networks underlying ethnic differences in tuberculosis risk., in the last oral presentation, sreedharan et al. [12] presented oqtans: a multifunctional, workbench for rnaseq data analysis. to assist the investigation of the abundance of rna transcripts and their potential differential expression, the workbench enables […]

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Oqtans institution(s)

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Machine Learning in Biology Group, Friedrich Miescher Laboratory, Tübingen, Germany; LINA, Combinatorics and Bioinformatics Group, University of Nantes, Nantes, France; Machine Learning/Intelligent Data Analysis Group, Technical University, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

Oqtans funding source(s)

Supported by Max Planck Society, the German Research Foundation (RA1894/1-1 and RA1894/2-1) and the Memorial SloanKettering Cancer Center (MSKCC).

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