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!
| 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. |
| 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. |
| 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. |
2013 A brief introduction to web-based genome browsers (Wang et al.)