Bio Protein Clustering Pangenome

Cluster proteins into orthogroups and derive pangenome matrices.

Instructions

1. Cluster proteins with MMseqs2 or ProteinOrtho.
2. Build presence/absence matrix.
3. Compute core/accessory/cloud/singleton partitions.
4. Identify single-copy orthologs for phylogenetic analysis.
5. Discriminate paralogs from orthologs in multi-copy gene families.
6. 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.md for 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.