Preprocessing Script Overview

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.

Subpages

• System Requirements: a list of the various libraries needed to run the preprocessing script
• Building SPQR Functionality: a guide to installing functionality to support the -spqr option on your system
  • Aside from the SPQR functionality, the rest of the preprocessing script is written solely in Python, so it should be portable for most operating systems.
  • However, invoking the SPQR functionality (-spqr) for the preprocessing script requires OGDF (a C++ library) and a C++ script to interface with the preprocessing script, 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 build this functionality for the preprocessing script.
• Options: detailed information about the various options available when running the script