Bandage: interactive visualization of de novo genome assemblies

By Ryan R. Wick, Mark B. Schultz, Justin Zobel, Kathryn E. Holt. Bioinform., 2015

2,534 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4143db924596b5ef39fe1cc9ea96fb97a6adfd9d

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In Molecular Biology

Citations in the corpus

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes (2018, methodology): “Meanwhile, the slimmed assembly graph (FASTG) and selected target assembly graph (GFA) can also be visualized by Bandage [30] to assess the completeness of the final”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, background): “Unicycler first assembles short reads into an accurate and connected assembly graph, a data structure containing both contigs and their interconnections[8].”
Completing bacterial genome assemblies with multiplex MinION sequencing (2017, methodology): “We used minimap to select ONT reads which corresponded to incomplete regions of the assembly, aligned these reads to the assembly graph using Bandage and BLAST, and chose the resolved assembly most compatible with the alignments [17, 18].”
Using SPAdes De Novo Assembler (2020, methodology): “To view FASTG and GFA files, we recommend using a Bandage visualization tool (Wick, Schultz, Zobel, & Holt, 2015).”
Sequence Analysis (2020, neutral): “We visualized assembly graphs using Bandage on CLOUDRNA SPA DES assembly graph.”
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities (2019, methodology): “We also provide an image of the assembly graph using Bandage (18), and assemblies can be polished using Racon (19) and Pilon (20) for long- and short-read assemblies respectively.”
A draft human pangenome reference (2022, neutral): “8.1, (Wick et al., 2015)).”
Plastid phylogenomics improve phylogenetic resolution in the Lauraceae (2020, methodology): “High‐quality short reads were viewed and edited using Bandage (Wick et al., 2015) to assemble a circular plastome.”