Scope: germline is general, somatic is human

These two halves of eidolon have deliberately different reach, and it is worth knowing which one you are using.

Germline simulation is species-agnostic. gen-reads needs a reference and, optionally, models trained from your own data — nothing in that path assumes a human genome. It has been exercised on H1N1 (13.5 kb, eight contigs), E. coli, yeast, soy, and human references from a single chromosome up to whole-genome GRCh38. If you are simulating germline variation for any organism, that is a supported use.

Somatic / cancer simulation is specialized to human. The bundled mutational models are derived from human cancer cohorts — COSMIC signatures and PCAWG structural-variant distributions — and the per-tissue models (BRCA, skin, lung) are human tissue types. SV size and type distributions, mutation rates, and signature weights all carry that provenance.

gen-cancer-reads will run against a non-human reference and produce output, but the model driving it has no meaning there: a yeast genome given a human pan-cancer SV spectrum produces numbers, not biology. We do not claim cancer simulation for non-human references, and the validation campaigns behind those models are human-only. Use another organism’s reference for cancer work only if you have trained your own models against matched data, and treat the bundled ones as human-specific.

This split is also why the two halves are validated differently: germline correctness is checked across deliberately varied contig shapes and sizes, while somatic realism is measured against real human sequencing data.