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Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0.

CIDANE: comprehensive isoform discovery and abundance estimation.

Author information

1
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
2
Toyota Technological Institute at Chicago, 6045 S. Kennwood Avenue, Chicago, IL 60637, USA.
3
Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany.
4
Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. david.weese@fu-berlin.de.
5
Department of Mathematics and Computer Science, Institute of Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. knut.reinert@fu-berlin.de.
6
Life Sciences, Centrum Wiskunde & Informatica (CWI), Science Park 123, Amsterdam, 1098 XG, The Netherlands. gunnar.klau@cwi.nl.

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

PMID:
26831908
PMCID:
PMC4734886
DOI:
10.1186/s13059-015-0865-0
[Indexed for MEDLINE]
Free PMC Article

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