IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data Article Swipe
Yalan Bi
,
Tom Lukas Lankenau
,
Matthias Lienhard
,
Ralf Herwig
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.jmb.2025.169049
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1016/j.jmb.2025.169049
Direct, single molecule measurement of RNA by long-read transcriptome sequencing (LRTS) enables the reliable detection of transcripts and alternative splicing events, thus contributing to the identification of splicing mechanisms, improvement of current gene models, as well as to the prediction of more reliable protein isoforms. LRTS data comes from either PacBio's single-molecule real time sequencing or from Oxford Nanopore's nanopore sequencing. Previously, we developed IsoTools, a software originally designed for processing and analyzing PacBio data. IsoTools copes with the complexity of LRTS data and offers multiple functionality for transcript identification and quantification as well as the analysis of differential isoform usage and local differential splicing events. Here, we report an update of the software, IsoTools 2.0, and demonstrate its additional performance on Oxford Nanopore data from multiple experimental protocols. We present the IsoTools 2.0 workflow, highlighting novel functionalities with respect to reliable transcript detection as well as transcription start site prediction. Additionally, we show novel metrics for structural description and quantification of gene model variability based on the gene's transcripts. We demonstrate the performance of IsoTools 2.0 on a variety of experimental protocols for library construction from a recent LRTS challenge. We show that IsoTools 2.0 is able to cope with the inherent complexity of LRTS data and that the workflow generates meaningful hypotheses on biomarkers for alternative splicing. The software is available from https://github.com/HerwigLab/IsoTools2/.
Related Topics
Concepts
Alternative splicing
Software
Computational biology
Workflow
Identification (biology)
Biology
RNA splicing
Nanopore sequencing
Gene
Computer science
Data mining
Genetics
Gene isoform
DNA sequencing
RNA
Database
Programming language
Botany
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.jmb.2025.169049
- OA Status
- hybrid
- Cited By
- 1
- References
- 26
- Related Works
- 10
- OpenAlex ID
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All OpenAlex metadata
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https://openalex.org/W4407947457Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.jmb.2025.169049Digital Object Identifier
- Title
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IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing DataWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-02-26Full publication date if available
- Authors
-
Yalan Bi, Tom Lukas Lankenau, Matthias Lienhard, Ralf HerwigList of authors in order
- Landing page
-
https://doi.org/10.1016/j.jmb.2025.169049Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
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hybridOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1016/j.jmb.2025.169049Direct OA link when available
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Alternative splicing, Software, Computational biology, Workflow, Identification (biology), Biology, RNA splicing, Nanopore sequencing, Gene, Computer science, Data mining, Genetics, Gene isoform, DNA sequencing, RNA, Database, Programming language, BotanyTop concepts (fields/topics) attached by OpenAlex
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1Total citation count in OpenAlex
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2025: 1Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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