Acknowledgements

This page describes the various libraries and programs used in (and used by) MetagenomeScope's code.

Preprocessing Script

• Graphviz and PyGraphviz
  • In particular, the dot and sfdp layout programs are used.
• NumPy
  • Used to calculate percentiles during edge thickness scaling.
• MetaCarvel
  • MetagenomeScope's version of spqr.cpp was derived from MetaCarvel's version of spqr.cpp.
• OGDF
  • Used to construct SPQR trees in spqr.cpp.
• cmdline.h
  • Used to parse command-line arguments in spqr.cpp.
• pysqlite
  • Used to create sqlite3 databases to be loaded in the viewer interface.
• futurize
  • Was used as a starting point when converting code from Python 2 to Python 3.
• pytest, pytest-cov
  • Used to test the preprocessing script.
• Flake8, Black
  • Used for style-checking and linting.

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.
• Mocha, Chai, mocha-headless-chrome, nyc
  • Used to test the viewer interface.
• Prettier, jshint
  • Used for style-checking and linting.
• csso-cli, UglifyJS, and html-minifier
  • Code minification.

Info Site

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

Test Data

See the README in the tests/ folder of this repository.

Miscellaneous

• Travis-CI
• Codecov

Code Links

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