splicekit: a comprehensive toolkit for splicing analysis from short-read RNA-seq

Zurich Seminars in Bioinformatics - Gregor Rot

  • 12:15 UZH Irchel Y55-l-06/08 and ZOOM Call

Abstract Splicing of RNA is a fundamental biological process. Dysregulation of splicing has been implicated in many human diseases and successfully exploited as a therapeutic target. Splicing analysis using short-read RNA-sequencing is a powerful technique to triage mechanism of action and safety profiles of drug candidates. There is, however, currently no comprehensive open-source software pipelines for such applications.

To address this need, we introduce splicekit, a Python package that provides a comprehensive set of splicing analysis tools. A prototypical pipeline built with splicekit starts with the identification of count data at the levels of junctions, exons and genes, and identifies regulated features. Downstream analysis includes sample clustering, event visualization, RNA-protein binding and sequence motif analysis to elucidate both cis and trans regulatory events involving regulated splice sites.

In summary, splicekit provides a user-friendly and powerful toolset for comprehensive splicing analysis from short-read RNA-seq data. We anticipate that it will be valuable for researchers in both basic and translational research of splicing modulation.

Welcome to visit #splicekit flash-talk and poster at ECCB 2023 in Lyon, France