Cidane

Cidane reconstructs and quantifies transcripts from RNA-seq reads for genome-based de novo transcript reconstruction and transcriptome quantification, integrating annotations of known splice sites, transcription start and end sites, and full-length transcripts.

Key Features:

• De novo transcript reconstruction: Reconstructs transcripts directly from RNA-seq reads without relying solely on existing gene models.
• Transcript quantification: Quantifies reconstructed transcripts from RNA-seq data.
• Integration of annotations: Incorporates known splice sites, transcription start sites, transcription end sites, and full-length transcripts into the reconstruction process.
• Gene-boundary data integration: Incorporates additional gene-boundary data to refine transcript structures.
• Splice-junction recovery: Recovers splice junctions that are often missed by other methods.
• Improved sensitivity and precision: Offers increased sensitivity and precision in assembling transcripts compared to existing tools.

Scientific Applications:

• Transcriptome reconstruction and quantification: Enables accurate reconstruction and quantification of transcriptomes from RNA-seq experiments.
• Novel splice-junction discovery: Identifies splice junctions and splice variants not captured by other methods.
• Gene expression studies across conditions: Supports analyses of gene expression patterns across different conditions or developmental stages.
• Annotation refinement for model organisms: Leverages available splice-site and full-length transcript annotations to improve transcript models in model organisms.

Methodology:

Reconstructs transcripts de novo from RNA-seq reads and integrates annotations of known splice sites, transcription start and end sites, full-length transcripts, and additional gene-boundary data for reconstruction and quantification.