THE NEW BANDAGE: As of version 2022.09, the Bandage tool is now built on `Bandage-NG <https://github.com/asl/BandageNG>`_. This fork of the original Bandage is better maintained with additional features and performance upgrades.
Bandage Overview
Bandage is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone.
Bandage works with Graphical Fragment Assembly (GFA) files. For more information about this file format, see here
Command Documentation
Bandage info takes a graph file (GFA) as input and outputs the following statistics about the graph:
Example output:
Node count: 561 Edge count: 734 Total length (bp): 4878380 Dead ends: 33 Percentage dead ends: 2.94118% Connected components: 19 Largest component (bp): 4821329 N50 (bp): 90360 Shortest node (bp): 1 Lower quartile node (bp): 17 Median node (bp): 87 Upper quartile node (bp): 404 Longest node (bp): 205425