Bio Protein Clustering Pangenome
Cluster proteins into orthogroups and derive pangenome matrices.
Instructions
- Cluster proteins with MMseqs2 or ProteinOrtho.
- Build presence/absence matrix.
- Compute core/accessory/cloud/singleton partitions.
- Identify single-copy orthologs for phylogenetic analysis.
- Discriminate paralogs from orthologs in multi-copy gene families.
- Calculate pangenome statistics (completeness, orthogroup occupancy).
Quick Reference
| Task | Action |
|---|---|
| Run workflow | Follow the steps in this skill and capture outputs. |
| Validate inputs | Confirm required inputs and reference data exist. |
| Review outputs | Inspect reports and QC gates before proceeding. |
| Tool docs | See docs/README.md. |
| References | See references.md and ../bio-skills-references.md. |
Input Requirements
Prerequisites:
- Tools available in the active environment (Pixi/conda/system). See
docs/README.mdfor expected tools. - Protein FASTA inputs are available. Inputs:
- proteins.faa (FASTA protein sequences)
Output
- results/bio-protein-clustering-pangenome/orthogroups.tsv
- results/bio-protein-clustering-pangenome/presence_absence.parquet
- results/bio-protein-clustering-pangenome/pangenome_report.md
- results/bio-protein-clustering-pangenome/logs/
Quality Gates
- Cluster size distributions meet project thresholds.
- Matrix completeness meets project thresholds.
- On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
- Verify proteins.faa is non-empty and amino acid encoded.
Examples
Example 1: Expected input layout
proteins.faa (FASTA protein sequences)
Troubleshooting
Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.
Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.