Acknowledgements

Preprocessing Script

• Graphviz and PyGraphviz
  • In particular, the dot and sfdp layout programs are used.
• NumPy
  • Used to calculate percentiles during edge thickness scaling.
• OGDF
  • Used to construct SPQR trees.
• cmdline.h
  • Used to parse command-line arguments in spqr.cpp.
• pysqlite
  • Used to create sqlite3 databases to be loaded in the viewer interface.

Viewer Interface

• sql.js
  • Used to read sqlite3 databases generated by the preprocessing script.
• Cytoscape.js
  • Used to render graphs.
  • Also, the toggling protocol and code used for the control panel of the viewer interface was inspired by a similar mechanism used in this Cytoscape.js demo (code repository here).
• jQuery
• Bootstrap
  • The icons used to theme various controls in the viewer application are from the Glyphicon Halflings set, included with Bootstrap.
  • The color selection functionality in the viewer interface uses the Bootstrap Colorpicker plugin.
  • Also, the markup used for the base of the modal dialogs in the viewer interface was adapted from Bootstrap's documentation on modals.
• csso/csso-cli, UglifyJS, and html-minifier are used to minify CSS, JS, and HTML code for the viewer interface, respectively.
• The JS code in loadajaxDB() in the viewer interface that performs an XMLHttpRequest was based on this article by Henry Algus.
• drawEdgeWeightHistogram() in the viewer interface's JS code was based on this example of using a D3.js histogram by Mike Bostock.

Info Site

See the README in the docs/ folder of this repository, where the code for the info site is stored.

Code Links

There are a couple of locations throughout MetagenomeScope's source code (in addition to the places mentioned above) where the solution was based on an article or example. These places are marked in the source code with a comment including the string CODELINK:, and should all contain a URL to their original source.