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Traph | A min-cost flow method for estimating transcript expression with RNA-Seq

Allows to identify and quantify transcript. Traph is a de novo genome-based tool with two-fold advantage: (i) it translates a problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers and (ii) it is general enough to encompass many of the previous proposals under the least sum of squares model. This method is based on network flows for a multi-assembly problem arising from isoform identification and quantification with RNA-Seq.

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Traph classification

Traph specifications

Unique identifier:
Software type:
Application/Script, Package/Module
Restrictions to use:
Computer skills:
Transcrips in gRAPHs
Command line interface
Operating system:

Traph distribution


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Traph support


  • Alexandru Tomescu <>
  • Anna Kuosmanen <>
  • Veli Makinen <>
  • Romeo Rizzi <>


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Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Finland; Department of Computer Science, University of Verona, Italy

Funding source(s)

Partially supported by Academy of Finland under grant 250345 (CoECGR).

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