How it works
Deterministic tools do the mechanical work. The agent does the interpretation — through a gated path.
The INDEX, the audit findings, the Phase‑6 candidate set, and the rendered HTML are byte‑deterministic for the same inputs. Interpretation is the agent's job, and it can only be written where the evidence gate allows.
Deterministic Python tools
Reproducible, mechanical, auditable. They build the genotype-truth INDEX, surface audit findings, assemble candidate sets, and render the final report — identical bytes, identical inputs.
Gated agent interpretation
The agent reads the tools' output and writes the plain-English meaning. Every clinical sentence must clear the evidence gate before it can be written to the page.
Genotype-truth INDEX
Build the source-of-truth index of observed genotypes straight from the raw chip.
ToolProvenance & claim audit
Scan prior documents for unsupported and aspirational claims against the INDEX.
ToolCross-document corrections
Reconcile contradictions across prior docs and rewrite them to the genotype truth.
Agent · gatedPharmacogenomics
Genotype-guided drug response, restated from CPIC / FDA PGx guidance.
Agent · gatedMTHFR / methylation
Methylation-cycle variants and downstream folate processing in context.
Agent · gatedProject-specific context
Apply the questions and focus areas particular to this subject's project.
Agent · gatedNet-new findings scan
Deterministic candidate set across ClinVar, ACMG SF, and CPIC for review.
ToolSummary & verification
Executive summary, then a final verification pass before the report is sealed.
Agent + verifyBuilt as two skills
A parsing substrate, and the audit pipeline that stands on it.
HelixlyAI ships as two sibling Claude Code skills. The decoder delegates every byte of parsing to the reader, so interpretation never touches a raw file directly.
genome-reader
Turns raw consumer exports into clean, queryable structures. It makes no clinical interpretation — it only reads, converts, and looks up.
- Format detection across 23andMe, AncestryDNA, MyHeritage
- Summary, rsID lookup, and region extraction
- VCF / Excel / QC conversion
- DNA → protein translation
genome-decoder
Runs the 8-phase workflow on top of the reader: it establishes genotype truth, audits prior documents, rebuilds them with citations, and renders the report.
- Builds a genotype-truth INDEX from the raw chip
- Audits prior docs for unsupported & aspirational claims
- Rebuilds with rsID + allow-list citations and a provenance block
- Renders the interlinked HelixlyAI HTML report
$GENOME_READER_PATH or the sibling directory.Evidence you can trace
Every clinical claim resolves to your genotype and a named source.
No claim reaches the page unless it can point to an rsID in your INDEX, an allow-list source, and a present-tense observation. Hover any finding in a HelixlyAI report and the chain is right there.
CYP2C19 — Intermediate Metabolizer
CPIC Level ATier 1rs4244285
chr10:96,541,616
G/A
The subject carries one *2 loss-of-function allele, observed as G/A at rs4244285 — a current finding of intermediate CYP2C19 activity. For affected substrates, exposure may differ from a normal metabolizer.
Cite an rsID in the INDEX
The claim must reference an rsID present in your genotype-truth INDEX, with the genotype actually observed on your chip.
Cite an allow-list source
Backed by an authoritative, pre-approved source — never an open-ended search or an unverifiable reference.
State a current observation
Present tense, about what is — never an aspiration, a hedge, or a maybe. Failing any rule means the sentence is not written.
Local, private, reproducible
Your DNA never leaves the machine. The report can be rebuilt byte-for-byte.
Runs locally
All parsing and rendering happen on your own machine. There is no HelixlyAI server in the loop.
Never uploaded, never committed
Your DNA export and the generated outputs are never sent off-device and never written to version control.
Reproducible by design
Same inputs + same allow-list snapshot date + same genome-reader version → the same report, every time.
Re-audit your genome analysis.
Install the two skills, point Claude Code at your export and prior documents, and ask it to rebuild and verify.
Not a diagnostic tool. Consult your prescribing clinician.
HelixlyAI restates guidance from authoritative sources — CPIC, the FDA PGx table, and peer-reviewed literature — and nothing more. It does not diagnose, and every clinical recommendation in a report ends with “consult your prescribing clinician.” Do not start, stop, or change any medication or treatment based on a HelixlyAI report.