Bandage: interactive visualization of de novo genome assemblies

Abstract

Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone.

Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage.

Contact: rrwick@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Fig. 1.

Examples of Bandage visualization (a) Left, ideal bacterial assembly (single contig); right, poor assembly with many short contigs. (b) Left, zoomed-in view of Salmonella assembly; repeated sequences (blaTEM and insertion sequence) appear as single nodes with multiple inputs and outputs. Node widths are scaled by read coverage (depth). Right, underlying gene structure deduced from Bandage visualization. (c) 16S rRNA region of a bacterial genome assembly graph, highlighted by Bandage’s integrated BLAST search. Nodes are labelled with their ID numbers and their widths are scaled by coverage. Even though the 16S gene failed to assemble into a single node, the user can manually reconstruct a complete dominant gene sequence from this succession of nodes: 175, 176, 64, 65 and 190