MetagenomeScope
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marbl
Visualization tool for (meta)genome assembly graphs
(The interactive visualization side of things still needs to be updated, so this isn't ready yet, but the DOT / stats export options both work.) ## Changes - MetagenomeScope now...
_From @fedarko on July 27, 2017 1:45_ From the comments of #10: "adding a command-line option to collate.py that, for a GFA/LastGraph/etc file, assumes that contigs are already oriented (and...
The "backfilling" algorithm means that edges are routed to the *center* head/tail-ports of collapsed structural patterns, rather than to individual nodes within these clusters. This results in edges getting weird...
These are the parameters for removing large components from the visualization. You can imagine a case where a component contains lots of nodes/edges, but a lot of them are collapsed...
For most of these, I can reuse most of the code -- the challenge will just be hooking things up properly. A lot of these can also be extended a...
Idea from Mihai: change the shapes -- so rather than showing two pentagons, one node is a triangle and the other one is a square (so it's still two nodes,...
If we allow cyclic bubbles (#241), then I guess we should also allow cyclic frayed ropes for the sake of consistency? I don't think this will mess with "interpretation" of...
To clarify, we still disallow cycles (including self-loop edges) _within_ bubbles. However, if there exists an edge (or edges, since we now allow multigraphs) from the end node to the...
So you can search for node IDs across any component in the graph (not just the current one). This should include the search functionality being enabled for the blank "no...
The current, hack-y way isn't great -- it just tiles the components vertically. Ideally we want to pack tiny components (e.g. just one or two nodes) that have relatively smaller...