PT  - JOURNAL ARTICLE
AU  - Stefan Canzar
AU  - Sandro Andreotti
AU  - David Weese
AU  - Knut Reinert
AU  - Gunnar W. Klau
TI  - CIDANE: Comprehensive isoform discovery and abundance estimation
AID  - 10.1101/017939
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 017939
4099  - http://biorxiv.org/content/early/2015/04/12/017939.short
4100  - http://biorxiv.org/content/early/2015/04/12/017939.full
AB  - We present CIDANE, a novel framework for genome-based transcript reconstruction and quantification from RNA-seq reads. CIDANE assembles transcripts with significantly higher sensitivity and precision than existing tools, while competing in speed with the fastest methods. In addition to reconstructing transcripts ab initio, the algorithm also allows to make 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 http://ccb.jhu.edu/software/cidane/.