Bandage

Bandage visualizes de novo assembly graphs to reveal contig nodes and edge connections for interpretation and analysis of genome assemblies.

Key Features:

• Graph visualization: Employs graph layout algorithms to render de novo assembly graphs showing contigs as nodes and connections as edges.
• Assembler compatibility: Accepts assembly graphs produced by assemblers such as Velvet, SPAdes, and MEGAHIT.
• BLAST integration: Performs BLAST sequence similarity searches and maps BLAST results onto graph nodes and edges.
• Sequence extraction: Extracts nucleotide sequences from assembly graph nodes (contigs).
• Implementation: Implemented in C++.

Scientific Applications:

• Genome structure interpretation: Visualizes connections between contigs to support interpretation of genomic architecture.
• Assembly error detection: Identifies ambiguous connections and potential misassemblies within de novo assemblies.
• Genetic variation exploration: Reveals alternative paths and structural variation present in assembly graphs.
• Comparative genomics and annotation: Maps BLAST hits onto graphs to assist comparative analyses and functional annotation.

Methodology:

Reads assembly graphs generated by assemblers such as Velvet, SPAdes, and MEGAHIT; applies graph layout algorithms to visualize nodes (contigs) and edges (connections); integrates BLAST searches and enables extraction of sequences from graph nodes; implemented in C++.