Repository: Freie Universität Berlin, Math Department

CIDANE: comprehensive isoform discovery and abundance estimation

Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X

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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 http://​ccb.​jhu.​edu/​software/​cidane/​.

Item Type:Article
Subjects:Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:1830
Deposited By: Anja Kasseckert
Deposited On:25 Feb 2016 12:27
Last Modified:15 Nov 2016 13:54

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