chadisaad / fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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 (coming soon)

Installation

From source

sudo apt-get install sqlite3 wget
python3 setup.py install

Usage

# Download required databases
# Currently supported databases: FusionGDB, 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/ 
  --ericscript tests/test_data/ericscript.tsv 
  --starfusion tests/test_data/starfusion.tsv 
  --fusioncatcher tests/test_data/fusioncatcher.txt
  --squid tests/test_data/squid.txt 
  --pizzly tests/test_data/pizzly.tsv
  --dragen tests/test_data/dragen.tsv

Or get help and list all possible parameters.

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

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

Credits

DNA icon made by Freepik from Flaticon is licensed by CC 3.0 BY.