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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:
OMICS_01279
Software type:
Application/Script, Package/Module
Restrictions to use:
None
Programming languages:
C++, Shell (Bash)
Computer skills:
Advanced
Maintained:
Yes
Name:
Mixed Integer Transcript IdEntification
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Stability:
Stable

MiTie distribution

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MiTie support

Maintainers

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

Credits

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Publications

Institution(s)

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.