Oqtans statistics

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Citations per year

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Popular tool citations

chevron_left Read alignment Normalization Differential expression De novo transcriptome assembly Bioinformatics workflows Novel transcript quantification Reference-based transcriptome assembly Spliced read alignment chevron_right
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Tool usage distribution map

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Associated diseases

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Oqtans specifications


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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  • person_outline Gunr Rätsch <>
  • person_outline Vipin Sreedharan <>

Publication for Online quantitative transcriptome analysis

Oqtans in publications

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 […]

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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