CIDANE: comprehensive isoform discovery and abundance estimation. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Canzar, Stefan; Andreotti, Sandro; Weese, David; Reinert, Knut; Klau, Gunnar
• Is Part Of: Genome biology. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 18
• Publication Date: 2016-12
• Subjects: Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-015-0865-0
• Languages: English
• ISSNs: 1474-760X

Abstract

Abstract 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 athttp://ccb.jhu.edu/software/cidane/ .