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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 forum

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Traph classification

Traph specifications

Unique identifier:
OMICS_01295
Software type:
Application/Script, Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Stability:
Stable
Name:
Transcrips in gRAPHs
Interface:
Command line interface
Operating system:
Unix/Linux
Version:
0.7.2
Maintained:
Yes

Traph distribution

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Traph support

Maintainers

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

Credits

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Publications

Institution(s)

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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