CIDANE: comprehensive isoform discovery and abundance estimation

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
Complete list of metadatas

Cited literature [38 references]  Display  Hide  Download

https://hal.inria.fr/hal-01397539
Contributor : Marie-France Sagot <>
Submitted on : Wednesday, November 16, 2016 - 9:30:37 AM
Last modification on : Wednesday, February 27, 2019 - 11:08:02 AM
Long-term archiving on : Thursday, March 16, 2017 - 1:50:58 PM

File

canzar2016.pdf
Publisher files allowed on an open archive

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar Klau. CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, BioMed Central, 2016, 17, pp.16. ⟨10.1186/s13059-015-0865-0⟩. ⟨hal-01397539v1⟩

Share

Metrics

Record views

101

Files downloads

34