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.