Viewer Interface Overview

MetagenomeScope's "viewer interface" is a client-side web application that can visualize database files generated by MetagenomeScope's preprocessing script. The viewer interface contains a variety of controls to assist in exploratory analysis and assembly finishing.

Browser Requirements

Any modern internet browser (with JavaScript enabled) should work fine for using the viewer interface. At present Google Chrome and Mozilla Firefox are recommended, since I haven't done a lot of testing on other browsers yet. (If you run into any problems using the viewer interface on your browser of choice, please let me know and I can look into it.)

Getting started

The viewer interface is just a normal client-side web application -- you shouldn't need to install anything in order to use it, assuming you're using a modern internet browser with Javascript enabled (as mentioned above). You can just open your browser to either the viewer interface demo or to a local copy of the viewer interface's HTML file, located in viewer/index.html in MetagenomeScope's code repository.*

Database files generated by the preprocessing script that are stored on your device locally can be loaded in the viewer interface using the "Upload .db file" button. In the demo of MetagenomeScope, a number of sample database files are available for you to try out using the "Demo .db file" button.

Once you've loaded a file, the "Draw connected component" buttons can be used to render a given connected component in the assembly graph represented by the database file in question. Note that connected components are automatically sorted in descending order of number of nodes -- so connected component 1 will be the largest, followed by 2, etc. In assembly graphs, the number of connected components in the "standard mode" view of the graph may be different from the number of connected components in the "decomposition mode" view of the graph -- see the "Assembly info" button for information on the number of connected components in each mode.

* If you just want to use a local copy of the viewer interface, you can download MetagenomeScope's code by running the following command:

git clone https://github.com/marbl/MetagenomeScope.git

Standard mode

This mode draws a normal view of the input graph, rendering each contig as either one (if contigs are assigned explicit orientations, as in a scaffold graph) or two (if contigs are not assigned explicit orientations) nodes. Edges between contigs are drawn accordingly.

In standard mode, structural patterns contained within the graph were automatically highlighted and grouped together during layout. These patterns can be easily identified by their background color and general structure.

Decomposition mode

In these modes, each biconnected component within the input graph is collapsed into the root node of its corresponding SPQR tree. These trees can then be iteratively expanded via right-clicking (similar to how node groups are collapsible/uncollapsible in standard mode).

In the "implicit" decomposition mode, expansions to the root node of a SPQR tree show iteratively larger amounts of detail added to the root. In the "explicit" decomposition mode, expansions actually result in the immediate descendant metanodes in the SPQR tree being drawn, revealing more and more of the literal SPQR tree structure for a given biconnected component.

Although "implicit" and "explicit" decompositions both show the same amount of nodes and edges upon first being drawn, the layouts involving explicit decomposition will usually be messier (since more space needs to be allocated for the SPQR tree structures) and will involve more nodes than their corresponding implicit decomposition upon fully being uncollapsed.