This FASTAG viewer appears very impressive (h/t: Anton). Have you used it?
De novo assembly graphs contain assembled contigs (nodes) but also the connections between those contigs (edges), which are not easily accessible to users. Bandage is a program for visualising assembly graphs using graph layout algorithms. By displaying connections between contigs, Bandage opens up new possibilities for analysing de novo assemblies that are not possible by looking at contigs alone.
A layout algorithm is used to automatically position graph nodes.
Manually reposition and reshape nodes.
Zoom, pan and rotate the view using either mouse or keyboard controls.
View the entire assembly graph or only a region of interest.
Copy node sequences to the clipboard or save them to file.
Nodes can be coloured using built-in colour schemes or user-defined colours.
Nodes can be labelled using node number, length, coverage or a user-defined label.
Find nodes quickly in a large graph using node numbers.
Specify the thickness of nodes and allow thickness to reflect the node’s coverage.
Define the relationship between the length of a node and the length of its sequence.
Two possible styles for handling reverse complement nodes:
Single: nodes and their reverse complements are drawn as one object with no direction.
Double: nodes are drawn using arrow heads to indicate direction and reverse complement nodes are drawn separately with arrow heads pointing the opposite direction.
Integrated BLAST search allows for highlighting specific sequences in an assembly graph.