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danejo3 edited this page Dec 2, 2024 · 27 revisions

Installation

Go to either the Bandage website or the GitHub releases page to download pre-built 64 bit executables for Mac, Windows or Linux. The Mac and Windows versions should come with all necessary libraries included and should work on OS X 10.7 or later and Windows 7 or later.

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, but it may be necessary to install the Qt5 package. 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.

Starting up the application

Note that, as somewhat unusual on Linux, the Bandage binary starts with a capital "B". So, to start it from the terminal, do the following, taking note of the capital "B":

Bandage &

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.

Supported formats

Bandage currently supports loading assembly graphs in the LastGraph format (used by Velvet), the FASTG format (used by SPAdes and MEGAHIT), the Trinity.fasta format (used by Trinity), the ASQG format (used by SGA and StriDe), and the GFA format (used by ABySS and other programs). If you are using IDBA, check out this tool for converting an IDBA graph into GFA format. See assembler differences for more information.

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 zip files containing pre-built Bandage binaries. 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 of the graph and the graph layout settings (see graph layout and appearance).

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 is advisable 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 or removes them from 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 can all be moved together.

Moving nodes

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

Zoom

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

Pan

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

Rotate

Touchpad navigation

If your OS and touchpad support these gestures (Macs and OS X do), they can be used in Bandage:

  • Two-finger scroll to pan the view.
  • Two-finger pinch to zoom in and out.
  • Two-finger rotate to rotate the view.
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.
  • Use Ctrl+Plus and Ctrl+Minus to zoom in and out.
  • Use arrow keys to pan the viewport horizontally and vertically.
  • Use Ctrl+Shift+Plus and Ctrl+Shift+Minus to rotate the view clockwise and anti-clockwise.
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