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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 (http://www.seqan.de), SAMtools (http://samtools.sourceforge.net/) and Bowtie2 aligner (http://bowtie-bio.sourceforge.net/bowtie2).

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