Canzar Stefan, Andreotti Sandro, Weese David, Reinert Knut, Klau Gunnar W
Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
Toyota Technological Institute at Chicago, 6045 S. Kennwood Avenue, Chicago, IL 60637, USA.
Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0.
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/.
我们展示了CIDANE，这是一个用于基于基因组的转录本重建和从RNA测序读数进行定量分析的新型框架。CIDANE能够高效地组装转录本，其灵敏度和精确度显著高于现有工具。它的算法核心不仅能从头开始重建转录本，还允许使用不断增加的已知剪接位点、转录起始和终止位点或全长转录本的注释信息，这些信息在大多数模式生物中都可获取。CIDANE支持对RNA测序和其他基因边界数据进行综合分析，并能发现其他方法无法检测到的剪接连接。可通过http://ccb.jhu.edu/software/cidane/获取CIDANE。
