CIDANE: Comprehensive isoform discovery and abundance estimation

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau

Research output: Contribution to journalArticlepeer-review

33 Scopus citations


We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts efficiently with significantly higher sensitivity and precision than existing tools. Its algorithmic core not only reconstructs transcripts ab initio, but also allows the use of the growing annotation of known splice sites, transcription start and end sites, or full-length transcripts, which are available for most model organisms. CIDANE supports the integrated analysis of RNA-seq and additional gene-boundary data and recovers splice junctions that are invisible to other methods. CIDANE is available at

Original languageEnglish (US)
Article number16
JournalGenome biology
Issue number1
StatePublished - Jan 30 2016

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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