What MetaPathways does
For the tool-by-tool diagrams and citations, see the detailed workflow.
The main workflow figure and the diagrams below share the appnote’s gray modules, blue inputs, green outputs and serif typography. Diamonds denote compute steps, not decisions; the schema diagram retains its relationship notation.
MetaPathways connects assembly annotations, read abundance and optional pathway inference in a shared set of sample and genome results. It accepts one sample or a collection and runs locally or through Slurm.
Assemblies are required. Reads add abundance measurements; genome assignments let MP split community annotations into genome-specific inputs. MP does not assemble reads or perform genome binning. Reports remain available when optional inputs are omitted.
For PGDBs, complete the Pathway Tools installation guide first. Use --skip_ptools to run without pathway inference. The data-flow diagram shows these dependencies in more detail.
Start with installation and the included three-sample test, then follow the complete workflow.