Genomic Foundation — Overview¶
Kind: engine · Demo: E1 · Source: core/engines/genomic-foundation
Illustrative. Genomic Foundation at a glance.
What it is¶
Turns raw sequencing reads into a list of the specific letters where a person's genome differs from the reference.
Why it matters¶
Every downstream answer — which variant, which drug, which trial — depends on this list being right.
Decision support for a qualified clinician — never autonomous diagnosis or prescribing. Every output on this page is intended to inform a clinician's judgement, not replace it.
Honest limit¶
Alignment and variant calling require NVIDIA Parabricks, which is not installed on this box. Results shown today are pre-computed.
Endpoints¶
:5000 — a single-service portal, so there is no separate API port
| Capability | Type | Status | Endpoint |
|---|---|---|---|
genomics-engine |
engine | live | localhost:5000 |
variant-store |
service | live | localhost:8575 |
mosaicism-vaf |
stage | planned | localhost:8575 |
acmg-secondary-findings |
stage | live | — |
gwas-association |
stage | live | — |
Size and health¶
| Python files | 15 |
| Lines of code | 3,264 |
| Test files | 8 |
| Containerised | yes |
Verify at any time:
.venv/bin/python scripts/run_all_tests.py genomic-foundation
Where to go next¶
- Foundation Learning Guide — the concepts, no prior knowledge assumed
- Advanced Learning Guide — architecture, modules, extension points
- Demo Guide — how to run
E1