RNA-seq denovo

De NGS Pipelines Wiki.



Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quiet diverse. This article presents an user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data.

Demo & Screenshots

A running version is available here where you can browse a demonstration project.


  • Installation guide - Which steps are required to setup the software package.
  • Process - How can I process (annot, align, variant detect...) my own data on the system.
  • Load - How can I load my own data on the system.
  • User interface - A full documentation helping the end-user to go throught the WEB interface.


You can find a tarball of the different versions here.

Announcing ...

  • RNAbrowse v.1.4 - Process SNPs annotations.
  • RNAbrowse v.1.3 - Add a workflow to process data starting from a contig file (performs annotations, variation detections and predictions).
  • RNAbrowse v.1.2 - Fixe several display bugs.
  • RNAbrowse v.1.1 - Fixe a bug with python 2.7.2 and when rerunning a workflow.
  • RNAbrowse v.1.0 - Here is the first packaged version of the tool.
  • Check out the poster we presented at the 2013 JOBIM Meeting in Toulouse.

How to cite

Mariette J, Noirot C, Nabihoudine I, Bardou P, Hoede C, Djari A, Cabau C, Klopp C. (2014) RNAbrowse: RNA-Seq De Novo Assembly Results Browser. PLoS ONE 9(5): e96821. doi: 10.1371/journal.pone.0096821

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