Browser viewer for pangenome graphs, at https://jbrowse.org/demos/bandagejs/
- Built for: pangenomes. Haplotype walks, bubbles, genes and regions cut from a walk file are first-class
- Also opens: de novo assembly graphs, as Bandage does
- In: a GFA (plain or gzipped), or a region cut live from a pangenome
- Out: a force-directed, anchored or tube-map drawing with haplotypes, bubbles and genes marked
- Open: File → Open, paste a url, drop a GFA on the page, or use
?gfa=<url> - Cut a region:
?walks=hprc&loc=chr6:160,614,798-160,647,758&haps=HG00097,HG00133. Paste a walk file url (or a gbz-base.gbz.db) to cut your own - Go to: type a region, position or gene name in the location box (
g); regions read 1-based, as JBrowse writes them - Inspect: click a node, or find it by name, for its links, walks, bubble and genes
- Haplotypes: highlight walks as lanes or side by side (details)
- Layout: the Layout menu picks force-directed, anchored, sample rows, walk rows, ordered, tube map or tube map on reference (details)
- Share: File → Copy link (parameters)
- Export: File → Export SVG (figures)
- Haplotypes: highlighting walks, panels and rows
- Layouts: each layout, what it needs and its settings
- Genes: gene tracks, assemblies and site setup
- Links: every address parameter
- Walk files: cutting regions from your own haplotypes
- Walk file tutorial: gfa-to-tabix to a cut, step by step
- Figures: SVG export and figure specs
- Gallery: example figures
- Developing: build, test, figures and deploy
- jbrowse-plugin-graphgenomeviewer: the JBrowse 2 plugin for these graphs
- HPRC tutorial
- @jbrowse/bandage-core (npm): layout
and drawing, plus
bandage-figurefor SVGs with no browser - @jbrowse/graph-stress-layout (npm): stress layout
- @gmod/gbz-base (npm):
.gbz.dbreader - @jbrowse/graph-walks (npm): walk file reader
- gfa-to-tabix: writes walk files
- ggbandage (R): Bandage-style figures as ggplot2 layers