BandageJS
BandageJS draws genome graphs in a web browser. Try it at
https://jbrowse.org/demos/bandagejs/, which opens on an example; the Examples
menu lists more.
The LPA gene in the HPRC human pangenome graph. Coloured nodes follow chr6 of
GRCh38, the human reference genome, from red to purple, and gold rings mark
LPA's exons. Dark grey nodes hold sequence that GRCh38 lacks, such as the 68.4
kb loop of extra KIV-2 repeat copies.
Genome graphs
- A genome graph stores DNA as sequence segments (nodes) joined by links
(edges). GFA is its file
format
- A pangenome graph holds many genomes, each haplotype as a walk: the
list of segments it passes through. Where genomes differ, their walks take
different branches
- Bandage draws de novo assembly graphs,
and BandageJS opens those too. It also highlights walks, marks where they
branch, draws genes on a reference genome, and reads one region at a time from
a whole-genome pangenome
Opening a GFA file
Drag a GFA file (.gfa or .gfa.gz) onto the page, or choose it in File →
Open. BandageJS loads the whole file, so this suits an assembly graph or a
pangenome graph of one region, like the examples. A whole-genome pangenome is
too large to load; see the next section.
Opening a region of a whole-genome pangenome
-
Index the GFA once with gfa-to-tabix
1.4 or later. --refs names the genome whose coordinates you will search by:
gfa-to-tabix graph.gfa --walks --refs GRCh38 -o graph
The command writes a walk file, graph.GRCh38.walks.bed.gz, and its index,
graph.GRCh38.walks.bed.gz.tbi. A graph shipped as .gbz, as HPRC's are,
converts to GFA first with vg convert -f graph.gbz > graph.gfa
-
Put both files on a web server that answers range requests and allows
cross-origin reads, as Amazon S3 does
-
Paste the .walks.bed.gz url into File → Open, then type a region of the
reference genome, such as chr6:160,614,798-160,647,758. BandageJS downloads
only the part of the file in that region
The HPRC release 2 human pangenome is hosted already:
open LPA from it.
Walk files covers these steps with screenshots. BandageJS
also reads regions from a gbz-base
database (.gbz.db) the same way.
Exploring and sharing
- Click a node for its details, or press
g and type a region or gene name
- Pick a layout from the Layout menu, and highlight
walks from the Haplotypes menu
- File → Copy link shares the view, and File → Export SVG saves it
Docs
- User guide: layouts, highlighting haplotypes, genes and every
address parameter
- Walk files: making a walk file and opening a region of
it, step by step
Gallery
More in the gallery.
See also
Libraries
License
GPL-3.0-or-later, building on BandageNG and
OGDF
