Bandage: interactive visualization of <i>de novo</i> genome assemblies

Abstract

Abstract Summary: 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.

Keywords

ContigComputer scienceBandageSource codeVisualizationGraphZoomFeature (linguistics)Sequence assemblySoftwareGraphical user interfaceProgramming languageTheoretical computer scienceGenomeData miningBiologyMedicine

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Publication Info

Year: 2015
Type: article
Volume: 31
Issue: 20
Pages: 3350-3352
Citations: 2815
Access: Closed

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APA Style

                            
                                
                                    Ryan R. Wick, 
                                
                                    Mark B. Schultz, 
                                
                                    Justin Zobel
                                
                                et al.
                            
                            (2015). 
                            Bandage: interactive visualization of <i>de novo</i> genome assemblies. 
                            Bioinformatics
                            , 31
                            (20)
                            , 3350-3352.
                            https://doi.org/10.1093/bioinformatics/btv383
                        

Identifiers

DOI: 10.1093/bioinformatics/btv383