IsoTools – a flexible workflow for long-read transcriptome sequencing analysis

Abstract Long-read transcriptome sequencing (LRTS) holds the promise to refine our understanding of alternative splicing, however, the nature of splicing is highly complex, and computational tools need to cope with this complexity by maximum flexibility at different steps of the work-flow. For this purpose we developed IsoTools, a Python-based LRTS analysis package. IsoTools provides broad functionality for transcriptome reconstruction and quantification of isoforms. Additionally, we implemented a graph-based method for the identification of alternative splicing events and a statistical approach based on the beta-binomial distribution for the detection of differential events. To demonstrate our methods, we generated PacBio LRTS data of human hepatocytes treated with the HDAC inhibitor valproic acid. Contrasted with short read RNA-seq, this analysis shows that LRTS provides valuable additional insights for a better understanding of alternative splicing, in particular with respect to complex novel and differential splicing patterns. IsoTools is available at https://github.com/MatthiasLienhard/isotools.