Acknowledgements

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

Preprocessing Script

Graphviz and PyGraphviz
NumPy
NetworkX
Click
GfaPy
pyfastg
Jinja
futurize
- Was used as a starting point when converting code from Python 2 to Python 3.
pytest, pytest-cov
Flake8, Black

Viewer Interface

Cytoscape.js
- 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).
- For collapsing/uncollapsing patterns, the "cytoscape-expand-collapse" extension is used.
jQuery
RequireJS
Underscore.js
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
Prettier, jshint

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

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.