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- Title
IsoTools: a flexible workflow for long-read transcriptome sequencing analysis.
- Authors
Lienhard, Matthias; van den Beucken, Twan; Timmermann, Bernd; Hochradel, Myriam; Börno, Stefan; Caiment, Florian; Vingron, Martin; Herwig, Ralf
- Abstract
Motivation Long-read transcriptome sequencing (LRTS) has the potential to enhance our understanding of alternative splicing and the complexity of this process requires the use of versatile computational tools, with the ability to accommodate various stages of the workflow with maximum flexibility. Results We introduce IsoTools, a Python-based LRTS analysis framework that offers a wide range of functionality for transcriptome reconstruction and quantification of transcripts. Furthermore, we integrate a graph-based method for identifying alternative splicing events and a statistical approach based on the beta-binomial distribution for detecting differential events. To demonstrate the effectiveness of our methods, we applied IsoTools to PacBio LRTS data of human hepatocytes treated with the histone deacetylase inhibitor valproic acid. Our results indicate that LRTS can provide valuable insights into alternative splicing, particularly in terms of complex and differential splicing patterns, in comparison to short-read RNA-seq. Availability and implementation IsoTools is available on GitHub and PyPI, and its documentation, including tutorials, CLI, and API references, can be found at https://isotools.readthedocs.io/.
- Subjects
ALTERNATIVE RNA splicing; SEQUENCE analysis; TRANSCRIPTOMES; HISTONE deacetylase inhibitors; WORKFLOW; WORKFLOW management systems; BINOMIAL distribution
- Publication
Bioinformatics, 2023, Vol 39, Issue 6, p1
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btad364