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MiTie | Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples

Offers a framework for transcriptome reconstruction. MiTie starts from a selection of a set of transcripts for determining and quantifying RNA-Seq-based transcript simultaneously in several samples. The software is a flexible application composed of two main steps: first it generates a splicing graph from RNA-Seq alignments, an annotation or both; second the software solves the core optimization problem.

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MiTie forum

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MiTie classification

MiTie specifications

Unique identifier:
Software type:
Application/Script, Package/Module
Restrictions to use:
Programming languages:
C++, Shell (Bash)
Computer skills:
Mixed Integer Transcript IdEntification
Command line interface
Operating system:
GNU General Public License version 3.0

MiTie distribution


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MiTie support


  • Jos Behr <>
  • Gunnar Rätsch <>
  • Jonas Behr <>


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Computational Biology Center, Sloan-Kettering Institute, New York, NY, USA; Friedrich Miescher Laboratory, Max Planck Society, Tubingen, Germany

Funding source(s)

Supported by the German Research Foundation (grants RA1894/1-1 and RA1894/2-1), the Sloan-Kettering Institute and the Max Planck Society.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.