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https://github.com/clinical-genomics/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/
https://github.com/clinical-genomics/fusion-report

fusion-genes report visualization

Last synced: 6 days ago
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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/

Host: GitHub
URL: https://github.com/clinical-genomics/fusion-report
Owner: Clinical-Genomics
License: gpl-3.0
Created: 2019-03-02T13:53:31.000Z (almost 6 years ago)
Default Branch: master
Last Pushed: 2024-11-28T14:37:14.000Z (24 days ago)
Last Synced: 2024-11-28T15:34:49.730Z (24 days ago)
Topics: fusion-genes, report, visualization
Language: Python
Homepage:
Size: 20.7 MB
Stars: 24
Watchers: 5
Forks: 10
Open Issues: 2
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE

Awesome Lists containing this project

README

        # ![fusion-report](https://raw.githubusercontent.com/matq007/fusion-report/master/fusion_report/templates/assets/img/fusion-report.png)

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/fusion-report/README.html)

![build](https://github.com/matq007/fusion-report/workflows/CI%20%5Bmaster%5D/badge.svg)

[![Codacy Badge](https://api.codacy.com/project/badge/Grade/932dff8661394cc28448af7b22748bb5)](https://app.codacy.com/app/mproksik/fusion-report?utm_source=github.com&utm_medium=referral&utm_content=matq007/fusion-report&utm_campaign=Badge_Grade_Dashboard)

[![DOI](https://zenodo.org/badge/173453958.svg)](https://zenodo.org/badge/latestdoi/173453958)

[![Slack Status](https://img.shields.io/badge/slack-join-brightgreen)](https://nf-co.re/join/slack)

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

> **TL;DR**: Live demo [here](https://matq007.github.io/fusion-report/example).

## Supported tools

* [STAR-Fusion](https://github.com/STAR-Fusion/STAR-Fusion)

* [EricScript](https://sites.google.com/site/bioericscript/)

* [Pizzly](https://github.com/pmelsted/pizzly)

* [Squid](https://github.com/Kingsford-Group/squid)

* [Dragen](https://emea.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html)

* [Arriba](https://github.com/suhrig/arriba)

* [Illumina Dragen](https://emea.illumina.com/products/by-type/informatics-products/dragen-bio-it-platform.html)

* [Jaffa](https://github.com/Oshlack/JAFFA)

## Installation

### Using Conda

```bash

conda install -c bioconda fusion-report=2.1.4

```

### From source

```bash

sudo apt-get install sqlite3

python3 setup.py install

```

## Usage

```bash

# Download required databases

# Currently supported databases: FusionGDB2, Mitelman and COSMIC

# COSMIC requires login credentials to download Fusion gene Database

fusion_report download --cosmic_usr '' --cosmic_passwd '' /path/to/db/

# Run the fusion-report

fusion_report run "" /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.

```bash

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](https://matq007.github.io/fusion-report/).

## Credits

* Testing dataset copied from [ndaniel/fusioncatcher](https://github.com/ndaniel/fusioncatcher).

* DNA icon made by [Freepik](https://www.freepik.com) from [Flaticon](https://www.flaticon.com) is licensed by [CC 3.0 BY](http://creativecommons.org/licenses/by/3.0/).