CTAT-LR-Fusion | Qin AIM Lab

CTAT-LR-Fusion is a long-read fusion transcript caller designed for PacBio and Oxford Nanopore isoform sequencing. It supports bulk and single-cell inputs, integrates short-read evidence when available, and produces high-confidence fusion calls with isoform-level resolution (Qin et al., 2025).

The tool addresses long-standing limitations of short-read fusion detection in complex tumor transcriptomes, including ambiguous junctions, repetitive sequence at breakpoints, and isoform diversity. It is integrated with the Trinity Cancer Transcriptome Analysis Toolkit (CTAT) and used in cancer transcriptomics studies that require accurate fusion characterization. Source code and documentation are available on GitHub.

References

2025

Genome Res

Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution

Qian Qin, Victoria Popic, Kirsty Wienand, and 11 more authors

Genome Research, Apr 2025

DOI Bib HTML

@article{Qin2025CTATLRFusion,
  title = {Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution},
  author = {Qin, Qian and Popic, Victoria and Wienand, Kirsty and Yu, Houlin and White, Emily and Khorgade, Akanksha and Shin, Asa and Georgescu, Christophe and Campbell, Catarina D and Dondi, Arthur and Beerenwinkel, Niko and Vazquez, Francisca and Al'Khafaji, Aziz M and Haas, Brian J},
  journal = {Genome Research},
  volume = {35},
  number = {4},
  pages = {967--986},
  month = apr,
  year = {2025},
  doi = {10.1101/gr.279200.124},
}