https://github.com/marianattestad/ribbon

A genome browser designed for complex structural variants and long reads.
https://github.com/marianattestad/ribbon

bioinformatics genome genomics visualization

Last synced: 10 days ago
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A genome browser designed for complex structural variants and long reads.

• Host: GitHub
• URL: https://github.com/marianattestad/ribbon
• Owner: MariaNattestad
• License: mit
• Created: 2016-06-30T00:31:33.000Z (almost 9 years ago)
• Default Branch: main
• Last Pushed: 2025-02-26T18:33:36.000Z (about 2 months ago)
• Last Synced: 2025-04-03T11:11:14.921Z (19 days ago)
• Topics: bioinformatics, genome, genomics, visualization
• Language: JavaScript
• Homepage: https://genomeribbon.com
• Size: 33.3 MB
• Stars: 280
• Watchers: 14
• Forks: 30
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# Ribbon/SplitThreader

Ribbon and SplitThreader are both visualization tools for exploring complex rearrangements and long-range structural variants. Especially if you have long reads, Ribbon and SplitThreader should be quite helpful for figuring out what's going on around large variants.

Ribbon is available online at [genomeribbon.com](https://genomeribbon.com)

## Major changes in 2024

[v2.0 release notes](docs/release_notes_v2.md)

![SplitThreader to Ribbon jumping demo](images/jump_splitthreader_to_ribbon.gif)

Both built by Maria Nattestad originally, we decided in 2024 to put Ribbon and SplitThreader together and give them both major updates. This was prompted by a collaboration with the Genome in a Bottle (GIAB) team at NIST to support the release of their somatic (tumor) benchmark dataset for HG008. 2024 development done by Maria Nattestad and Robert Aboukhalil.

## Documentation

* How to read the visualizations? Check out [interpretation](docs/interpretation.md) for examples.

* What changed in 2024? Including how to make a session with multiple files: [v2.0 release notes](docs/release_notes_v2.md)

## Citation and publications

Please cite our paper in [_Bioinformatics_](https://doi.org/10.1093/bioinformatics/btaa680).

The BioRxiv has both the [Ribbon preprint](https://www.biorxiv.org/content/10.1101/082123v1) and the [SplitThreader preprint](https://www.biorxiv.org/content/10.1101/087981v1.full).

### Ribbon

![Ribbon overview](images/ribbon_overview.png)

### SplitThreader

![SplitThreader overview](images/splitthreader_overview.png)

There are several algorithms available within SplitThreader that can help make sense of long-range rearrangements, from categorizing variants:

![](images/splitthreader_variant_categories_diagram.jpg)

to searching for gene fusions:

[gene fusion algorithms described in supplement to SplitThreader preprint](https://www.biorxiv.org/content/biorxiv/suppl/2016/11/15/087981.DC1/087981-1.pdf).

## Local deployment

If you need to run Ribbon/SplitThreader without internet access, go to releases and find the ribbon_splitthreader.zip bundle from the latest release.

```bash

unzip ribbon_splitthreader.zip

cd ribbon_splitthreader

python3 -m http.server

# or run any other server pointed at that directory.

```

Note that permalinks won't work without internet access.

## Development and building from source

To develop new features in Ribbon, first install [npm](https://www.npmjs.com/get-npm).

Then clone this repository and build it:

```bash

# Clone repo and install dependencies

git clone https://github.com/marianattestad/ribbon

cd ribbon

npm install

# to run locally for development

npm run dev

# to build from source:

npm run build

npm run serve # to test the build

# To run a server with this build:

cd dist

python3 -m http.server

```