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.
conda install -c bioconda fusion-report# sqlite3 can be installed via conda/mamba as well sudo apt-get install sqlite3 pip3 install -r requirements.txt && python3 setup.py install# 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 --helpFor more info on how to run the script, please see the documentation.
- Testing dataset copied from ndaniel/fusioncatcher.
- DNA icon made by Freepik from Flaticon is licensed by CC 3.0 BY.