Golden Helix isn't a black box. Custom report templates, evaluation scripts, REST APIs, CLI automation, and native LIMS integration let you tailor every step of the pipeline to your lab.
From branded clinical reports to programmatic API access, Golden Helix provides the hooks to integrate with your existing infrastructure and tailor outputs to your lab's standards.
Design branded, ACMG-compliant clinical reports with styleable templates. One-click generation converts analysis results into PDF or XML—no manual transcription, no formatting errors.
VSWarehouse exposes a performant REST API with full OpenAPI (Swagger) documentation for standardized, tooling-friendly integration and data exchange. VSPipeline provides command-line control over the full analysis engine for scripted batch processing and scheduling.
Connect your analysis pipeline to laboratory information systems, electronic health records, and billing platforms. Import sample data, export structured results, and automate reconciliation workflows.
Data flows through a validated chain from external systems into analysis and back out to downstream consumers—all through documented, versioned interfaces.
LIMS systems push sample metadata and sequencing data into VSWarehouse via REST API or watched file directories. Support for FASTQ, VCF, and structured metadata imports.
Evaluation scripts automate ACMG scoring, custom annotation sources add institutional knowledge, and project templates encode validated filtering chains—all configurable per assay.
VSReports converts analysis output into branded clinical documents. Choose from ACMG-standard templates or build custom layouts with your institutional branding, exported as PDF or XML.
Structured results flow back to LIMS, EHR, and billing systems via REST API. Hospital systems query VSWarehouse for report counts, patient results, and reconciliation data.
Explore Related Capabilities
Clinical reporting and annotation configuration are first-class features of the platform, not afterthoughts. Every report template, annotation source, and evaluation script is fully customizable.
Styleable HTML-to-PDF templates that match your institutional identity. Include HGVS nomenclature, coverage data, pathogenicity assessments, and OMIM gene summaries automatically.
Add institutional variant catalogs, custom frequency databases, and proprietary scoring models alongside curated public sources. VarSeq treats them identically in filtering workflows.
Automate ACMG scoring criteria, custom classification logic, and variant triage rules. Scripts execute within the validated pipeline, reducing manual steps while maintaining clinical auditability.
Our team will help design the integration architecture that fits your institutional requirements.
Every integration point is designed for production use in regulated clinical environments—versioned, documented, and audit-ready.
Bidirectional data exchange with external systems. Query patient reports, import sample metadata, export structured results, and automate reconciliation workflows.
Full programmatic access to the VarSeq analysis engine. Schedule batch jobs, trigger analyses on new data arrival, and integrate with existing bioinformatics schedulers.
Clinical reports in PDF for distribution. XML for LIMS integration. JSON and multi-tab Excel for downstream systems. Saved Exports to Catalogs for dynamic, scalable result management.
How labs use the customization and integration capabilities to fit Golden Helix into their existing workflows.
Sample metadata flows from LIMS into VSWarehouse. VSPipeline runs the validated analysis template. Branded reports are generated and exported back to LIMS—hands-free.
Hospital billing systems query VSWarehouse for report counts per patient. EHR platforms receive structured genomic results via API, supporting HL7 and FHIR data exchange workflows.
Core facilities serving diverse research and clinical programs connect upstream variant callers and sequencing platforms into a single VSWarehouse instance with standardized analysis and reporting.
Technical guides, API documentation walkthroughs, and expert webcasts on building connected genomic workflows.
See how Golden Helix integrates with your LIMS, EHR, and existing bioinformatics pipelines.