Awesome Genome Browsers
April 30, 2019 ยท View on GitHub
This repo is for keeping track of genome browsers and genomic visualization tools. The initial list is taken from twitter replies, Google-ing, and my memory.
I'd love pull requests!
Reactive Genome Browsers (web)
| Tool | Manuscript | Comments |
|---|---|---|
| igv.js | - | JavaScript based tools from the IGV team. Super easy to get started. A bit barebones in functionality for track picking and plotting. Actively developed (as of April 2019) |
| jbrowse | Genome Biology | JavaScript / HTML5 tool. Actively developed (as of April 2019). They also have a Electron desktop tool. Good looking docs, tons of features. |
| higlass | Genome Biology | D3.js based 2D (Hi-C) and 1D genome browser. Can handle hundreds of tracks. Actively developed (as of April 2019). Docker app for deployment. |
| GIVE | Genome Biology | 1D browser with some "2D" (Hi-C) data functionality. Docker install option. |
Reactive Genome Browsers (desktop)
| Tool | Manuscript | Comments |
|---|---|---|
| epiviz | Nature Methods | R / bioconductor tool. From quick reading of docs, I don't see how this can be deployed on a personal server. Last update late 2018. |
| IGV | Briefings in Bioinformatics | The benchmark for desktop tools. |
Genome Visualization (static)
| Tool | Manuscript | Comments |
|---|---|---|
| ggbio | Genome Biology | R / bioconductor tool. gg for ggplot grammar. |
| Gviz | Statistical Genomics | R / bioconductor tool. Handles many data types. Good docs. |
| karyoploteR | Bioinformatics | R / Bioconductor tool. As name suggests, most examples are genome-wide with karyoplots / ideograms with some overlaid data. |
Discussions
2013 A brief introduction to web-based genome browsers (Wang et al.)