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Multi-Organism Support

sr2silo supports processing samples from multiple organisms with organism-specific reference sequences.

Supported Organisms

Organism Identifier Description
COVID-19 covid SARS-CoV-2 / Severe acute respiratory syndrome coronavirus 2
RSV-A rsva Respiratory Syncytial Virus A
RSV-B rsvb Respiratory Syncytial Virus B

Reference Resolution

sr2silo resolves reference sequences in the following priority order:

  1. Local References (fastest): resources/references/{organism}/
  2. LAPIS Instance: Fetched from specified --lapis-url if available
  3. Fallback: Local references as final fallback if LAPIS fetch fails

This allows for both static local references and dynamic references from a LAPIS instance.

Usage

For detailed usage, see:

sr2silo process-from-vpipe --help

The --organism parameter specifies which organism to process. Can also be set via ORGANISM environment variable (CLI argument takes precedence).

Adding New Organisms

To add support for a new organism:

  1. Add reference files to resources/references/{organism_id}/:

  2. nuc_ref.fasta - Nucleotide reference sequence(s)

  3. aa_ref.fasta - Amino acid reference sequences for gene annotations
  4. Use GenBank parser (if starting from GenBank format):

python scripts/extract_gbk_references.py \
    reference.gbk \
    --nuc-output resources/references/{organism_id}/nuc_ref.fasta \
    --aa-output resources/references/{organism_id}/aa_ref.fasta
3. Update configuration:

  • Add your organism's column mappings to a `timeline_columns.yml` file and pass it via `--timeline-config` (or `TIMELINE_CONFIG` env var) — no new release needed
  • Update workflow config.yaml with your new organism ID
  • Update documentation with organism details

  • Test (optional):

  • Add test fixtures in tests/conftest.py

  • Add parameterized tests in tests/test_main.py

Workflow Integration

Specify organism in workflow/config.yaml:

ORGANISM: "covid"  # or "rsva"

Troubleshooting

Reference files not found:

  • Verify files exist: ls resources/references/{organism}/
  • Check organism identifier spelling
  • Use --lapis-url to fetch from LAPIS
  • Generate from GenBank: python scripts/extract_gbk_references.py --help