December 2020: MetagenomeScope is back! We just merged in a new version of the codebase featuring many new features, including hierarchical pattern decomposition, bubble boundary duplication, drawing multiple components at once, and much more. Check out the code and installation instructions on GitHub!
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)!
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 a visualization interface (a client-side web application). The preprocessing script takes as input an assembly graph file (currently LastGraph, GFA, FASTG, and MetaCarvel GML files are accepted) and creates a directory containing the HTML / JS / CSS visualization.
MetagenomeScope is still under active development, so please get in touch with us if you have any questions or other feedback about the tool.
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.
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.