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Bandage: interactive visualization of de novo genome assemblies.

Wick RR, Schultz MB, Zobel J, Holt KE - Bioinformatics (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne and.

No MeSH data available.


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
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btv383-F1: 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

Mentions: Assemblies of whole genomes can be difficult to complete if repeated sequences occur in chromosomes or plasmids. Repeated sequences cause distinctive structures in the assembly graph, limiting contig length. Bandage’s visualization of the assembly graph makes it easy to identify such problematic parts of assemblies (Fig. 1a). In some cases, it is possible to manually resolve these ambiguities by using additional information not available to the assembler. Bandage facilitates this by allowing users to copy sequences directly from the graph visualization. In other cases, ambiguities cannot be resolved and the assembly cannot be completed. For these situations, Bandage provides a clear illustration of the assembly’s incompleteness and comparison of one assembly’s quality to another.Fig. 1.


Bandage: interactive visualization of de novo genome assemblies.

Wick RR, Schultz MB, Zobel J, Holt KE - Bioinformatics (2015)

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
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595904&req=5

btv383-F1: 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
Mentions: Assemblies of whole genomes can be difficult to complete if repeated sequences occur in chromosomes or plasmids. Repeated sequences cause distinctive structures in the assembly graph, limiting contig length. Bandage’s visualization of the assembly graph makes it easy to identify such problematic parts of assemblies (Fig. 1a). In some cases, it is possible to manually resolve these ambiguities by using additional information not available to the assembler. Bandage facilitates this by allowing users to copy sequences directly from the graph visualization. In other cases, ambiguities cannot be resolved and the assembly cannot be completed. For these situations, Bandage provides a clear illustration of the assembly’s incompleteness and comparison of one assembly’s quality to another.Fig. 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne and.

No MeSH data available.