Scientific Methods — Multi-genome Comparison

Input & annotation

A collection contains 3–20 assemblies with distinct input hashes and labels. Prokka annotates each assembly with --kingdom Bacteria and 2 CPUs, generating the GFF inputs for Panaroo.

Uncompressed .fasta, .fa or .fna bacterial assemblies. Each file is limited to 25,000,000 bytes, 100,000–20,000,000 sequence bases and at most 10,000 contigs. Validation checks non-empty records, unique record identifiers and IUPAC DNA symbols.

Gene families & presence/absence

Panaroo performs pan-genome family clustering on the Prokka GFF files with --clean-mode moderate, --core_threshold 0.95 and 4 threads. The product mode is Multi-genome comparison; pan-genome describes the scientific method.

For N submitted genomes, a core family is observed in at least ceil(0.95 × N) genomes. A genome-specific family occurs in one genome. Accessory families occur in at least two genomes but below the core threshold. These definitions refer only to the submitted collection.

The full binary presence/absence matrix is exported. The heatmap displays up to 60 variable families, ordered by prevalence then family identifier; core families are shown if no variable families exist. A displayed subset is not the full matrix.

Delivered outputs

Report and ZIP include family annotations, presence/absence matrices, core/accessory/genome-specific tables, assembly and annotation summaries, heatmap, Panaroo technical outputs, methods, tool versions, manifest and checksums. Source assemblies are excluded.

Interpretation & limitations

Family calls depend on assembly completeness, annotation and clustering. A family not detected in an assembly is not proof of biological absence. Genome-specific means specific within this collection, not unique across the species. This mode does not establish phylogeny or clinical significance.