Screenshot of MetagenomeScope's 'standard mode' with bubbles, frayed ropes, and chains visible.

Screenshot of MetagenomeScope's "standard mode," zoomed in on a region of a biofilm assembly graph.

Screenshot of MetagenomeScope's 'explicit' SPQR tree decomposition mode, showing the full structure of a SPQR tree.

Screenshot of MetagenomeScope's "explicit" SPQR tree decomposition mode, generated for the figure 2a graph in [Nijkamp, Pop, Reinders, de Ridder 2013].

News

August 2018: Gave a presentation and tutorial on MetagenomeScope during the 2018 Strategies and Techniques for Analyzing Microbial Population Structures (STAMPS) course at the Marine Biological Laboratory! Check out the slides here, and check out the command-line MetagenomeScope tutorial here.

January 2018: Presented a poster on MetagenomeScope at the 2018 Winter Mid-Atlantic Microbiome Meetup (M3)!

September 2017: Presented a poster on MetagenomeScope at GD 2017! Check out the poster here.

Overview

MetagenomeScope is a web-based visualization tool designed for metagenomic assembly graphs. MetagenomeScope aims to display a semi-linearized, hierarchical overview of the input graph while emphasizing the presence of certain structural patterns in the graph.

The tool consists of a preprocessing script (written in Python and C++) and a viewer interface (a client-side web application). The preprocessing script takes as input an assembly graph file (currently LastGraph, GFA, and MetaCarvel GML graphs are accepted) and outputs a SQLite database file containing the layout information for the graph's connected components. This database file can be visualized in the viewer interface.

MetagenomeScope is still under active development, so please get in touch with us if you have any questions or other feedback about the tool.

Features

Demo

A demo of MetagenomeScope's viewer interface (with about a dozen sample database files available for use) is available online at mgsc.umiacs.io. You can also upload your own database files generated by the preprocessing script to visualize them in the tool.

Documentation

Documentation on downloading, running, and using MetagenomeScope is available in its GitHub wiki, located here. The wiki is a work in progress, so if you have any further questions please feel free to contact us.

Code

The source code for MetagenomeScope is publicly available on GitHub here. MetagenomeScope is licensed under the GNU General Public License, version 3. (If you're interested, the source code for this site is also available on GitHub.)

See the acknowledgements section of MetagenomeScope's wiki for an up-to-date list of the third-party libraries used by MetagenomeScope.

Contact

MetagenomeScope was created by members of the Pop Lab in the Center for Bioinformatics and Computational Biology at the University of Maryland, College Park.

Feel free to email mfedarko (at) umd (dot) edu with any questions, suggestions, comments, concerns, etc. regarding the tool. If you'd like, you can also open an issue on MetagenomeScope's GitHub page.