Bandage

The application visualises de novo assembly graphs, showing connections that are absent from contig files and thereby extending the analyst’s view of assembly structure. It supports several graph formats—including LastGraph, FASTG, Trinity.fasta, ASQG and GFA— and automatically positions nodes with an efficient layout algorithm. Users can navigate the graph by zooming, panning, rotating, or dragging nodes, and can limit the view to the whole assembly or a specific region of interest.

Features include copying or saving node sequences, colour‑coding nodes with built‑in or custom schemes, and labelling by number, length, coverage or user‑defined tags. Nodes can be displayed in single‑ or double‑node styles, with thickness reflecting read depth, and integrated BLAST search highlights and labels specific sequences. Command‑line access allows batch loading of settings, and image generation.

The tool is intended for bioinformaticians who need to assess assembly quality, locate problematic regions, resolve ambiguities, and extract candidate sequences spanning multiple nodes. It runs on macOS, Linux and Windows as a portable 64‑bit binary requiring no installation, with optional source builds for custom environments.