**Bandage: Interactive Visualization of De novo Genome Assemblies** **Authors:** Ryan R. Wick, Mark B. Schultz, Justin Zobel, and Kathryn E. Holt **Abstract:** Bandage is a tool designed to visualize de novo genome assembly graphs, which are typically represented as de Bruijn graphs. These graphs contain contigs (long sequences) and edges (connections between contigs). Bandage allows users to interact with the graph by zooming, panning, moving nodes, adding labels, changing colors, and extracting sequences. It also supports BLAST searches within the graphical user interface, displaying hits as highlights in the graph. This visualization approach provides new insights into de novo assemblies that are not possible with contigs alone. **Implementation and Performance:** Bandage is a C++ application using Qt, ensuring speed, memory efficiency, and cross-platform compatibility (Linux, OS X, Windows). It uses the Open Graph Drawing Framework for graph layout, which scales well for large graphs. On a 3 GHz laptop, Bandage can load and display a bacterial genome assembly (5 Mb) in seconds with minimal RAM usage. For larger assemblies (100 Mb+), performance and memory requirements increase, but Bandage can still handle them by focusing on specific regions. **Features and Case Studies:** - **Assembly Quality and Completion:** Bandage helps identify problematic parts of assemblies due to repeated sequences, allowing users to manually resolve ambiguities. - **Resolving Complex Antibiotic Resistance Regions:** Bandage aids in investigating the composition of *Salmonella* genomic islands (SGIs) by visualizing connections between contigs, facilitating the determination of gene presence. - **16S rRNA Sequence from a Bacterial Assembly:** Bandage's BLAST integration highlights the 16S gene in the assembly graph, enabling users to reconstruct the entire gene sequence from fragmented contigs. **Conclusion:** By visualizing both nodes and edges, Bandage provides users with detailed access to the connection information in assembly graphs, particularly useful for assemblies with many short contigs. This tool enhances the analysis and assessment of de novo assemblies. **Acknowledgements:** The authors thank Simon Gladman and Jane Hawkey for their testing and feedback during Bandage’s development. **Conflict of Interest:** None declared.**Bandage: Interactive Visualization of De novo Genome Assemblies** **Authors:** Ryan R. Wick, Mark B. Schultz, Justin Zobel, and Kathryn E. Holt **Abstract:** Bandage is a tool designed to visualize de novo genome assembly graphs, which are typically represented as de Bruijn graphs. These graphs contain contigs (long sequences) and edges (connections between contigs). Bandage allows users to interact with the graph by zooming, panning, moving nodes, adding labels, changing colors, and extracting sequences. It also supports BLAST searches within the graphical user interface, displaying hits as highlights in the graph. This visualization approach provides new insights into de novo assemblies that are not possible with contigs alone. **Implementation and Performance:** Bandage is a C++ application using Qt, ensuring speed, memory efficiency, and cross-platform compatibility (Linux, OS X, Windows). It uses the Open Graph Drawing Framework for graph layout, which scales well for large graphs. On a 3 GHz laptop, Bandage can load and display a bacterial genome assembly (5 Mb) in seconds with minimal RAM usage. For larger assemblies (100 Mb+), performance and memory requirements increase, but Bandage can still handle them by focusing on specific regions. **Features and Case Studies:** - **Assembly Quality and Completion:** Bandage helps identify problematic parts of assemblies due to repeated sequences, allowing users to manually resolve ambiguities. - **Resolving Complex Antibiotic Resistance Regions:** Bandage aids in investigating the composition of *Salmonella* genomic islands (SGIs) by visualizing connections between contigs, facilitating the determination of gene presence. - **16S rRNA Sequence from a Bacterial Assembly:** Bandage's BLAST integration highlights the 16S gene in the assembly graph, enabling users to reconstruct the entire gene sequence from fragmented contigs. **Conclusion:** By visualizing both nodes and edges, Bandage provides users with detailed access to the connection information in assembly graphs, particularly useful for assemblies with many short contigs. This tool enhances the analysis and assessment of de novo assemblies. **Acknowledgements:** The authors thank Simon Gladman and Jane Hawkey for their testing and feedback during Bandage’s development. **Conflict of Interest:** None declared.