This python script generates an interactive summary report from fusion detection tools. Fusion-report is part of a bigger project nf-core/rnafusion which is designed to detect and report fusion genes from RNA-seq data.

TL;DR: Live demo here.

Supported tools

• STAR-Fusion
• EricScript
• Pizzly
• Squid
• Dragen
• Arriba
• Illumina Dragen
• Jaffa
• CTAT-LR-Fusion

Installation

Using Conda

conda install -c bioconda fusion-report

From source

# sqlite3 can be installed via conda/mamba as well
sudo apt-get install sqlite3
pip3 install -r requirements.txt && python3 setup.py install

Usage

# Download required databases
# Currently supported databases: FusionGDB2, Mitelman and COSMIC
# COSMIC requires login credentials to download Fusion gene Database
fusion_report download --cosmic_usr '<username>' --cosmic_passwd '<password>' /path/to/db/

# Run the fusion-report
fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
  --arriba tests/test_data/arriba.tsv \
  --dragen tests/test_data/dragen.tsv \
  --ericscript tests/test_data/ericscript.tsv \
  --fusioncatcher tests/test_data/fusioncatcher.txt \
  --pizzly tests/test_data/pizzly.tsv \
  --squid tests/test_data/squid.txt \
  --starfusion tests/test_data/starfusion.tsv \
  --jaffa tests/test_data/jaffa.csv \
  --allow-multiple-gene-symbols # in case gene symbol in fusion can't be determined, treat each provided fusion as a separate one.

Or get help and list all possible parameters.

fusion_report --help
fusion_report run --help
fusion_report download --help
fusion_report sync --help

For more info on how to run the script, please see the documentation.

Credits

• Testing dataset copied from ndaniel/fusioncatcher.
• DNA icon made by Freepik from Flaticon is licensed by CC 3.0 BY.