RefShannon

RefShannon assembles genome-guided transcriptomes from RNA-Seq short reads to reconstruct isoform-level transcripts and resolve alternative splicing by exploiting transcript abundance variation.

Key Features:

• Genome-Guided Approach: Uses a genome-guided strategy to map RNA-Seq short reads and assemble them into transcripts.
• Abundance-Aware Assembly: Leverages variations in transcript abundance to distinguish and accurately reconstruct different isoforms.
• Handling Alternative Splicing: Resolves complex alternative splicing events to enable isoform-level reconstruction from a single gene.
• Improved Sensitivity: Demonstrates up to 22% improved sensitivity at a given specificity in comparative evaluations against other transcriptome assemblers.
• Python Implementation: Implemented in Python.

Scientific Applications:

• Isoform-level analysis: Reconstruction of individual transcript isoforms for downstream analyses.
• Gene expression quantification: Supports quantification of transcript-level expression from RNA-Seq data.
• Alternative splicing studies: Identification and characterization of alternative splicing events.
• Transcript diversity exploration: Exploration of transcriptome complexity and diversity within genomic loci.

Methodology:

Performs genome-guided assembly by mapping and stitching RNA-Seq short reads and exploits transcript abundance variation to distinguish and reconstruct isoforms.