MetaPathways
Annotate metagenomes, measure read abundance, infer community and genome pathways, and explore the results. Run on a local server or submit work through Slurm using the same commands.
New users: start with installation and the three-sample test. The small input dataset and workflow helpers are included. Want PGDBs? Follow the Pathway Tools installation guide before running the complete workflow.
Arrows between numbered modules trace the conceptual flow of results; independent tasks and optional branches follow the dependencies in the detailed workflow. Optional reads add abundance; genome maps add genome-specific analysis. The report and explorer connect available results for searching, subsetting and CSV export. View the SVG · Detailed workflow and citations.
Start simple
Run your analysis
Analysis guides
- Organize assemblies, reads and genome assignments
- Prepare reference databases
- Pathway Tools: licensing, image builds, databases and inference
- Complete multi-sample analysis
- Annotate your own data
- MAGs and pathway inference
- Command cookbook: run only the modules you need
- Resources and Slurm
- Logs, temporary files and restarting
- Troubleshooting and reproducibility
Understand and explore
Results and reference
- Explore results, follow links and export tables
- Reports and the EDA portal
- Results schema and EDA portal
- Software architecture: local and HPC
- Data flow: inputs to connected results
- Detailed workflow and tool citations
- Workflow and output guide
- Complete CLI reference
- Benchmarking and supplementary statistics
- Reproducibility and validation
Maintain and contribute
Development
Source code and documentation: GitHub. Questions, bugs and feature requests: GitHub issues. See the README for contributors and citation.