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Ryan Wick edited this page Sep 7, 2015 · 28 revisions

Installation

Go to either the Bandage website or the GitHub releases page to download pre-built binaries for Mac, Windows or Linux. The Mac and Windows versions should come with all necessary libraries included.

The Linux version is available in two flavours: dynamically-linked, which does not contain the GUI code, and statically-linked, which does. The dynamically-linked version is preferable, as it will use native GUI components. It may work immediately on modern Linux distributions, or it may be necessary to install the Qt5 library. The statically-linked version of Bandage has fewer dependencies, but uses non-native GUI components.

It is also possible to build Bandage from source – the instructions are in the Bandage readme.

In-application help

Many items in Bandage have a help icon next to them: help text icon. Click these to read a description of that part of Bandage.

Load a graph

Before you can do anything else in Bandage, you must load an assembly graph. Do this by choosing 'Load graph' from the 'File' menu.

Load graph

If you need a graph to examine, a small sample graph is included in the Bandage binary zip files. You can also download a couple of other graphs here: * [An _E. coli_ genome assembly from Velvet](http://rrwick.github.io/Bandage/samples/E_coli_LastGraph.zip) * [A small mouse transcriptome from Trinity](http://rrwick.github.io/Bandage/samples/Trinity.fasta.zip)

Small graphs should load quickly, though it may take some time for very large assembly graphs to load (see working with very large graphs).

Draw the graph

After the graph is loaded, you can click the 'Draw graph' button to draw the graph to the screen. This step performs the graph layout, and the time it takes depends on the size and complexity of the graph.

Draw graph

For smaller graphs, such as a bacterial genome, drawing the entire graph is usually feasible. However, for a larger graph, such as a metagenome or eukaryote assembly, it may be necessary to reduce the graph scope before drawing the graph (see graph scope).

Controls

Note that on a Mac, the Command key is used instead of the Ctrl key in the below instructions.

Selection
  • Click on any node or edge to select it.

Selecting nodes

* Holding Ctrl while clicking on nodes or edges adds them to the selection.

Selecting nodes

* Click and drag to select large numbers of nodes and edges.

Selecting nodes

Moving nodes
  • Left click and drag on any node to move it. For short nodes, this will move the entire node. For long nodes, this will move the region of the node near the mouse cursor.

Moving nodes

* Right click and drag on any node to move it one piece at a time. This is useful for fine tuning the shape of a graph or for rotating short nodes.

Moving nodes

* Selected nodes are moved in their entirety when dragged. If multiple nodes are selected, they will all be moved together when dragged.

Moving nodes

Mouse navigation
  • Ctrl+mouse wheel will zoom the view in to and out from the location of your mouse cursor.

Zoom

* Ctrl+click and drag with the left mouse button will pan the view.

Pan

* Ctrl+click and drag with the right mouse button will rotate the view.

Rotate

Keyboard navigation controls
  • It is first necessary to click in the viewport (or use tab until it is selected) so it will receive keyboard input.
  • Plus and minus keys will zoom in and out.
  • Arrow keys will pan the viewport horizontally and vertically.
  • Shift+plus and shift+minus will rotate the view clockwise and anti-clockwise.

More information

Take a look at these other wiki pages for more detailed information on Bandage functionality:

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