Swan

Swan analyzes and visualizes transcript isoforms from long-read RNA-sequencing data (PacBio, Oxford Nanopore) to identify novel splice variants and differential transcript expression.

Key Features:

• Visualization and analysis: Provides visualization and analysis of complex transcript models generated from long-read RNA-sequencing data.
• Differential expression detection: Detects differentially expressed transcripts between conditions, exemplified by identification of 4,909 differentially expressed transcripts between HepG2 and HFFc6, including 279 transcripts whose parent genes were not differentially expressed.
• Novel isoform discovery: Identifies novel splicing events such as exon skipping and intron retention, including 1,021 reproducible exon-skipping events and 73 intron-retention events not present in the GENCODE v29 annotation.

Scientific Applications:

• Isoform-level expression analysis: Quantifying and comparing transcript isoform expression to reveal isoform-specific regulation.
• Splicing and novel isoform discovery: Detecting exon-skipping, intron-retention, and previously unannotated transcript variants relative to reference annotations such as GENCODE v29.
• Comparative transcriptomics: Comparing transcriptomes across cell types or conditions to identify differentially expressed transcripts and condition-specific isoforms.

Methodology:

Implemented in Python 3.