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.
- STAR-Fusion
- EricScript
- Pizzly
- Squid
- Dragen
- Arriba (coming soon)
sudo apt-get install sqlite3 wget
python3 setup.py install
# 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.
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