Auditable Germline WGS Processing
Genomatis Core is the genomic processing layer for the qualified Illumina germline WGS workflow. It accepts FASTQ, BAM, and CRAM only when the runtime capability manifest marks the format available, then exposes authoritative QC metrics, pipeline stages, provenance, checksums, and verified VCF or gVCF artifacts. Clinical interpretation, variant classification, and report authoring are downstream responsibilities of Genomatis Interpret and are not performed by Core.
Capability-Gated Intake
The backend format manifest and pipeline capability registry determine what can be uploaded and what can execute. The UI blocks submission when readiness evidence is absent.
Durable Genomic Uploads
Resumable multipart transfer, explicit FASTQ R1/R2 declarations, complete-content validation, and server-issued SHA-256 receipts protect the intake chain.
Qualified Germline WGS
The current release exposes the Illumina germline whole-genome workflow only, with a server-owned reference and fail-closed workflow, storage, and executor checks.
Operational Traceability
Authoritative job and stage status, persisted provenance, checksums, QC metrics, and verified artifact manifests make every completed run auditable.
Clear Product Boundary
Core processes genomic data and publishes verified outputs. Genomatis Interpret performs downstream interpretation, classification, review, and clinical report workflows.
| Release area | Genomatis Core | Boundary / evidence |
|---|---|---|
| Supported assay | Illumina germline WGS | Other assays remain unavailable until separately qualified |
| Accepted intake | FASTQ, BAM, and CRAM when runtime-declared available | File validation does not imply pipeline executability |
| Execution gate | Workflow, reference, storage, and executor readiness | Submission is blocked when any required check is unhealthy |
| Upload integrity | Durable multipart sessions and server SHA-256 receipts | Pairing is explicit; filenames are never treated as evidence |
| Monitoring | Authoritative job and stage status through polling | No synthetic realtime state or fabricated execution logs |
| Outputs | Verified VCF or gVCF, indexes, QC, provenance, and checksum artifacts | Only server-published artifact manifests are downloadable |
| Downstream clinical work | Handed to Genomatis Interpret | Classification and report authoring are outside Core |