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TransRate
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TransRate

Transrate is a tool to assess and analyze de novo RNA-seq transcriptome assemblies. Transrate does not need a reference genome, and the report comprises analyses of structural errors, chimeras, incorrect bases, and deficient assembly. The algorithm uses unique statistics, the TransRate contig score, and the TransRate assembly score.



TransRate

Transrate is a tool to assess and analyze de novo RNA-seq transcriptome assemblies. Transrate does not need a reference genome, and the report comprises analyses of structural errors, chimeras, incorrect bases, and deficient assembly. The algorithm uses unique statistics, the TransRate contig score, and the TransRate assembly score.

Topic

Transcriptome; Assembly; RNA-seq; Quality affairs

Details

  • Operation: Quality control report
  • Input: FASTA
  • Output: -
  • Software interface: Command-line user interface
  • Language: Ruby, C++
  • Operating system: Mac OS X, Linux
  • License: The MIT License
    • Cost: Free
  • Version name: 1.0.3
    • Maturity: Stable
  • Credit: The Millennium Seed Bank (Royal Botanical Gardens, Kew), Royal Society University Research, Biotechnology and Biological Sciences Research Council (BBSRC), Department for International Development, Bill & Melinda Gates Foundation, Sustainable Crop Production Research for International Development programme, the Department of Biotechnology of the Government of India's Ministry of Science and Technology, the European Union's Horizon 2020 research and innovation program.
  • Contact: Steven Kelly steven.kelly _at_ plants.ox.ac.uk
  • Collection: -

Publications

Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S "TransRate: reference-free quality assessment of de novo transcriptome assemblies." Genome Res. 2016 Aug;26(8):1134-44. https://doi.org/10.1101/gr.196469.115
PMID: 27252236
PMCID: PMC4971766


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