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InFusion is a toolkit for fusion gene and chimeric transcript detection from RNA-seq data. It is capable of detecting a large spectrum of chimeric RNAs including alternatively spliced fusion isoforms and fusions that involve intronic, non-coding or intergenic regions. Both single-end and paired-end reads are supported.

The toolkit provides the following features:

  • Discovery of fusions on transcript level, including splice-variants of a fusion
  • Support for detection of chimeras involving intronic and intergenic regions
  • Anti-sense transcription detection for strand-specific datasets
  • Scripts to integrate and compare results of different fusion-detection tools
  • A set of tools for fusion post-analysis
  • Simulation of RNA-seq data for fusion gene and chimeric transcript

InFusion is written in C++ and Python. It uses SeqAn library 1.4 (, SAMtools ( and Bowtie2 aligner (

The latest version is 0.8 (Released 16.03.2017)

Publication to cite: K. Okonechnikov et al "InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data"

Providing suggestions/reporting bugs/asking questions is possible by writing in InFusion google group or creating an issue in the repository.

In these studies InFusion was successfully applied for the analysis of RNA-seq data:

Lancet Oncology 2017 DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis

Nature 2018 Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Cancers 2019 Identification of Targetable Lesions in Anaplastic Thyroid Cancer by Genome Profiling

More citations here

For detailed information about code licensing please refer to the LICENSE.

Getting Started

User Manual


Public datasets analysis

Frequently Asked Questions