splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq

Abstract

Abstract Motivation Analysis of alternative splicing using short-read RNA-seq data is a complex process that involves several steps: alignment of reads to the reference genome, identification of alternatively spliced features, motif discovery, analysis of RNA-protein binding near donor and acceptor splice sites, and exploratory data visualization. To the best of our knowledge, there is currently no integrative open-source software dedicated to this task. Results Here, we introduce splicekit, a Python package that provides and integrates a set of existing and novel splicing analysis tools for conducting splicing analysis. Availability and implementation The software splicekit is open-source and available at Github (https://github.com/bedapub/splicekit) and via the Python Package Index.