LongTREC presents:
IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data
Yalan Bi, Tom Lukas Lankenau, Matthias Lienhard, Ralf Herwig
A single gene can produce several different RNA versions, or isoforms, by joining its pieces in different combinations, a process called alternative splicing. Long-read transcriptome sequencing reads each RNA molecule in one go, making it possible to see these isoforms directly. But the resulting data are complex, and researchers need dedicated software to turn millions of reads into reliable information.
The authors previously developed IsoTools, software originally designed for PacBio data. They now present IsoTools 2.0, which also works with Oxford Nanopore data from multiple experimental protocols. The new version improves transcript detection, predicts where transcription starts, and introduces new metrics that describe how variable a gene’s transcripts are. They tested it on data from different library preparation methods produced for a recent long-read benchmarking challenge.
IsoTools 2.0 copes with the complexity of long-read data and generates meaningful hypotheses about splicing changes that could serve as biomarkers. Freely available on GitHub, it gives the community a versatile tool for exploring transcript diversity, whichever long-read technology they use.
Read the full text here: https://doi.org/10.1016/j.jmb.2025.169049
