Traph specifications

Information


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

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Versioning


No version available

Maintainers


  • person_outline Alexandru Tomescu
  • person_outline Anna Kuosmanen
  • person_outline Veli Makinen
  • person_outline Romeo Rizzi

Publications for Transcrips in gRAPHs

Traph citation

library_books

Benchmark analysis of algorithms for determining and quantifying full length mRNA splice forms from RNA seq data

2015
Bioinformatics
PMCID: 4673975
PMID: 26338770
DOI: 10.1093/bioinformatics/btv488

[…] widely used. Other methods are StringTie (), Scripture (), Trinity (), Oases (Velvet) (), Soap-denovo-trans (), iReckon (), CLASS (), FlipFlop (), IsoLasso (), MiTie (), Trans-ABySS (), AUGUSTUS (), Traph ().Algorithms are classified by whether they use an alignment to a reference genome sequence, or whether they assemble the reads into full transcripts de novo by identifying overlapping reads. W […]

Traph institution(s)
Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Finland; Department of Computer Science, University of Verona, Italy
Traph funding source(s)
Partially supported by Academy of Finland under grant 250345 (CoECGR).

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