A tool to detect and visualize target gene fusions by scanning FASTQ files directly. This tool accepts FASTQ files and reference genome as input, and outputs detected fusion results in TEXT, JSON and HTML formats.
Take a quick glance of the informative report
- Sample HTML report: http://opengene.org/GeneFuse/report.html
- Sample JSON report: http://opengene.org/GeneFuse/report.json
- Dataset for testing: http://opengene.org/dataset.html
Get genefuse program
This binary is only for Linux systems, http://opengene.org/GeneFuse/genefuse
# this binary was compiled on CentOS, and tested on CentOS/Ubuntu wget http://opengene.org/GeneFuse/genefuse chmod a+x ./genefuse
or compile from source
# get source (you can also use browser to download from master or releases) git clone https://github.com/OpenGene/genefuse.git # build cd genefuse make # Install sudo make install
You should provide following arguments to run genefuse
- the reference genome fasta file, specified by
- the fusion setting file, specified by
- the fastq file(s), specified by
--read1=for single-end data. If dealing with pair-end data, specify the read2 file by
--html=to specify the file name of HTML report
--json=to specify the file name of JSON report
- the plain text result is directly printed to STDOUT, you can pipe it to a file using a
genefuse -r hg19.fasta -f genes/druggable.hg19.csv -1 R1.fq.gz -2 R2.fq.gz -h report.html > result
The reference genome should be a single whole FASTA file containg all chromosome data. This file shouldn't be compressed. For human data, typicall
hg38/GRch38 assembly is used, which can be downloaded from following sites:
hg38/GRch38: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz Remember to decompress hg38.fa.gz since it is gzipped and is not supported currently.
The fusion file is a list of coordinated target genes together with their exons. A sample is:
>EML4_ENST00000318522.5,chr2:42396490-42559688 1,42396490,42396776 2,42472645,42472827 3,42483641,42483770 4,42488261,42488434 5,42490318,42490446 ... >ALK_ENST00000389048.3,chr2:29415640-30144432 1,30142859,30144432 2,29940444,29940563 3,29917716,29917880 4,29754781,29754982 5,29606598,29606725 ...
The coordination system should be consistent with the reference genome.
Fusion files provided in this package
Four fusion files are provided with
genes/druggable.hg19.csv: all druggable fusion genes based on
genes/druggable.hg38.csv: all druggable fusion genes based on
genes/cancer.hg19.csv: all COSMIC curated fusion genes (http://cancer.sanger.ac.uk/cosmic/fusion) based on
genes/cancer.hg38.csv: all COSMIC curated fusion genes (http://cancer.sanger.ac.uk/cosmic/fusion) based on
genefuseruns almost ~5X faster with
druggablegenes are only a small subset of
cancergenes. Use this one if you only care about the fusion related personalized medicine for cancers.
cancergenes should be enough for most cancer related studies, since all COSMIC curated fusion genes are included.
- If you want to create a custom gene list, please follow the instructions given on next section.
Create a fusion file based on hg19 or hg38
If you'd like to create a custom fusion file, you can use
scripts/gen_fusion_file.jl, which is based on the Julia library
OpenGene.jl to generate the fusion file you want.
You should prepare a file containing all genes you want, seperated by
line break. Please note that
comma is not supported. Each gene should be the HGNC standard name.
By default, the primary transcript (named as GENE_001) will be used. But you can specify the transcript by add
_TranscriptId to the gene. For example: use
CD74_ENST00000009530 to specify the transcript of
When the gene list file (
genes.txt) is prepared, you can used following command to generate a fusion file (
julia scripts/gen_fusion_file.jl -r hg19 -g genes.txt -f fusion.csv
The reference genome is specified by
-r option, which can be hg19/GRch37/GRch38.
GeneFuse can generate very informative and interactive HTML pages to visualize the fusions with following information:
- the fusion genes, along with their transcripts.
- the inferred break point with reference genome coordinations.
- the inferred fusion protein, with all exons and the transcription direction.
- the supporting reads, with all bases colorized according to their quality scores.
- the number of supporting reads, and how many of them are unique (the rest may be duplications)
A HTML report example
See the HTML page of this picture: http://opengene.org/GeneFuse/report.html
options: -1, --read1 read1 file name (string) -2, --read2 read2 file name (string [=]) -f, --fusion fusion file name, in CSV format (string) -r, --ref reference fasta file name (string) -u, --unique specify the least supporting read number is required to report a fusion, default is 2 (int [=2]) -d, --deletion specify the least deletion length of a intra-gene deletion to report, default is 50 (int [=50]) -h, --html file name to store HTML report, default is genefuse.html (string [=genefuse.html]) -j, --json file name to store JSON report, default is genefuse.json (string [=genefuse.json]) -t, --thread worker thread number, default is 4 (int [=4]) -?, --help print this message
If you used GeneFuse in you work, you can cite it as:
Shifu Chen, Ming Liu, Tanxiao Huang, Wenting Liao, Mingyan Xu and Jia Gu. GeneFuse: detection and visualization of target gene fusions from DNA sequencing data. International Journal of Biological Sciences, 2018; 14(8): 843-848. doi: 10.7150/ijbs.24626