RT Journal Article
SR Electronic
T1 CIDANE: Comprehensive isoform discovery and abundance estimation
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 017939
DO 10.1101/017939
A1 Stefan Canzar
A1 Sandro Andreotti
A1 David Weese
A1 Knut Reinert
A1 Gunnar W. Klau
YR 2015
UL http://biorxiv.org/content/early/2015/04/12/017939.abstract
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/.