Edit in GitHub

GFusion is a software package to detect fusion genes using RNA-Seq data.

Download the latest version of GFusion. Version: 1.0.0. Last Modified: 2016-2-19

Download here

Authors: Qi Chen, Xiaofeng Song (

You can also modify, edit GFusion, and give us your suggestions and comments in GitHub, or by email.


perl -o out_file -r 0 -p 6 -i /path/to/bowtie1_index -g /path/to/genes.gtf -1 PE_reads_1.fastq -2 PE_reads_2.fastq


-o: output file directory;

-r: the expected (mean) inner distance between mate pairs(default = 0);

-n: the minimum number of split reads(default = 1);

-p: threads (default = 4);

-i: genome index (use bowtie index);

-g: gene annotation file(*.gtf file);

-1: pair-end reads file, PE_reads_1.fq

-2: pair-end reads file, PE_reads_2.fq;

-f: single-end reads file, SE_reads.fq;

-help: usage help;

-d: the minimum length of adjacent genes (default = 50000); ;

-L: the anchor length (more than 20bp, default = 0.4*read_length);


The following files (genome index file, gene annotation gtf file) could be download from TopHat. Website:


perl -o out_file -r 0 -p 6 -i hg19.fa -g genes.gtf -1 test_1.fastq -2 test_2.fastq

Example files download:

1. The alignment index file (-index): BowtieIndex files (Homo_sapiens, hg19 version) can be downloaded from;

2. The genome annotation file (-gtf): gtf file

3. Input file -- The fastq format file (zip file): test fastq file

4. Output file -- The reported Fusion genes list : Fusion genes list file

Software Prerequisites:

The following three software should be installed in your cluster or computer before running the

TopHat: a fast splice junction mapper for RNA-Seq reads;

Bowtie1: an tool for aligning sequencing reads to long reference sequences. Download and extract Bowtie 1 releases;

Samtools: utilities for the Sequence Alignment/Map (SAM) format;

Bioperl: a community effort to produce Perl code which is useful in biology.

Output file format:

GFusion will report the fusion genes in the out_file/result file. The information of fusion genes is listed as follow format:

1. 5’ gene name

2. 5’ chromosome

3. 5’ position

4. 3’ gene name

5. 3’ chromosome

6. 3’ position

7. strand

8. the number of split reads

9. the number of spanning reads


Qi Chen, Ping Han, Xiaofeng Song. GFusion: a Novel Algorithm to Identify Fusion Genes from Cancer RNA-Seq Data. (under review in peer-reviewed journal)


Copyright (C) 2016 Xiaofeng Song.