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Preprocessing Script Overview
Marcus Fedarko edited this page Jan 13, 2018
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MetagenomeScope's "preprocessing script" is a program that takes as input an assembly graph file and produces a SQLite database file that can be visualized in MetagenomeScope's viewer interface.
The preprocessing script is located in the graph_collator/ directory of MetagenomeScope. The script can be run with the command python graph_collator/collate.py.
- System Requirements: a list of the various libraries needed to run the preprocessing script
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Installation: a guide to installing the "SPQR version" of the script on your system
- The "non-SPQR version" of the script is written solely in Python, so that version of the script is relatively portable.
- However, the "SPQR version" of the preprocessing script uses OGDF (a C++ library) and a C++ script to interface with it, in order to generate SPQR tree decompositions for MetagenomeScope's "decomposition mode." So there are a few extra steps to compiling the C++ script to work on your system, in order to install this version of the preprocessing script.
- Settings: information about the various options available when running the script
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Controls
(Work in progress)
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Viewer Interface Tutorial