From sequencing readsto interpretable variants
Analyze FASTQ data, annotate variants, apply evidence-guided classification, and generate traceable reports in one secure genomic workspace.
No credit card required · 2 free analysis runs each month · Setup in minutes
NA12878_wes
Whole exome · Paired-end · 42.3M reads
Report generates automatically
Structured TSV + PDF on completion
- FASTQ / BAM / VCF workflows
- Reproducible run records
- Variant annotation
- Exportable reports
- Encrypted storage
Built for the teams behind Genome analysis
Genomics pipelines weren't built to move fast — most are still hand-assembled.
Aligners, callers, annotators, and a lab's own scripts, stitched together run after run. The cost shows up as hours nobody planned for.
Fragmented tooling
Aligners, callers, annotators, and custom scripts get stitched together by hand for every run, with no shared source of truth across the team.
Slow manual review
Cross-referencing every variant against clinical significance, population frequency, and disease-gene knowledge bases to apply ACMG criteria consistently takes hours a lab can't always spare.
Infrastructure overhead
Each lab re-solves compute, storage, and reproducibility from scratch instead of focusing on the science.
From FASTQ to a classified report - one ATGCFLOW, start to finish.
Quality control, alignment, variant calling, annotation, and ACMG/AMP-aligned classification run as a single orchestrated workflow - so your team reviews results instead of assembling the pipeline.
One reproducible pipeline
Every stage runs through a single orchestrated workflow - no manual handoffs between tools.
Evidence-based classification
Every ACMG call lists the exact criteria met (PVS1, PM2, PP3...) and why.
Cross-checked results
Automated classifications can be checked against an independent classification engine.
Encrypted by default
Uploaded reads and results are protected with encrypted storage and access controls.
Before vs. after ATGCFLOW
Manually chaining alignment, calling, and annotation scripts
One run, fully orchestrated
Cross-referencing databases by hand per variant
ACMG/AMP evidence applied automatically
Ad hoc file storage, no access controls
Encrypted, access-controlled storage by default
Wherever you sit in the workflow - the platform meets you there.
Whether you're running a research study, supporting a clinical workflow, or operating shared sequencing infrastructure - here's where to start.
Researchers
Run batch analysis for population studies, novel variant discovery, and biomarker research on standardized, reproducible pipelines.
- Batch processing of multiple samples
- Custom gene panel filtering
- Export ready for publication
Clinical & Diagnostic Labs
A research-use pipeline for rare disease and cancer genomics workflows, with ACMG/AMP-aligned classification and structured reporting.
- ACMG/AMP 2015 evidence-based classification
- Structured, exportable variant reports
- Encrypted storage & access controls
Core Facilities & Bioinformatics Teams
Plug WES analysis into existing infrastructure with consistent, auditable pipeline runs from raw FASTQ to classified variants.
- Reproducible, auditable pipeline runs
- Best-practices alignment & variant calling
- Job tracking and downloadable artifacts
Everything the workflow needs.
Automated Pipeline
Orchestrated QC through variant calling, with no manual handoffs between stages.
- Reproducible, auditable runs
- Scatter-gather parallelization
- Resumes from any failed step
Multi-Source Annotation
Every variant cross-referenced against population, clinical, and functional sources.
- Population frequency data
- Clinical significance
- Functional impact predictions
| Gene | Variant | Consequence | Population frequency | Review state |
|---|---|---|---|---|
| BRCA1 | c.5266dupC | Frameshift | Rare | Review required |
| TP53 | c.743G>A | Missense | Rare | Review required |
ACMG Classification
Every call evaluated against ACMG/AMP evidence criteria, with the underlying reasoning shown.
- Evidence-based scoring
- Independent cross-check engine
- Manual override, always
- Population evidence
- Computational evidence
- Functional evidence
- Clinical database evidence
- Literature evidence
Interactive Genome Browser
Inspect reads, coverage, and calls without leaving the platform.
- Real-time BAM/VCF viewing
- Coverage depth visualization
- Multi-sample comparison
Coverage depth
Read alignment
Position on chromosome 17
Whole Exome Sequencing, live today
Research beta focuses on WES end-to-end. Additional assay types below are on the product roadmap - not available in the workspace yet.
Whole Exome Analysis
Paired-end exome from FASTQ through variant calling, annotation, and research classification.
Assay roadmap
Planned expansions - not shipped. Contact us if a specific assay matters to your lab.
CNV Analysis
Copy-number signals from exome or panel depth profiles.
Somatic Cancer
Tumor-aware variant analysis for research oncology studies.
RNA-seq Expression
Bulk transcript quantification and differential expression.
scRNA-seq
Single-cell expression and clustering for research datasets.
Long-Read Sequencing
Structural-variant-aware analysis for long reads.
AI-assisted interpretation is coming to ATGCFLOW
We're building AI-assisted variant interpretation as a research-use capability, currently under active evaluation for reproducibility and privacy safeguards before it ships. Nothing below is live yet - here's what's on the roadmap.
Pipeline configuration assistance
Suggest sensible parameters for your sample type instead of hand-tuning config files.
Variant prioritization
Surface the variants most likely to matter for a given phenotype or gene panel.
Report drafting
Draft narrative summaries for review, grounded in the classified variant evidence.
Literature-grounded reasoning
Pull relevant literature context into variant review instead of manual lookups.
By the numbers
Every run measured the same way, against the same best-practices workflow.
Built with clinical data in mind
Genomic and health data deserves infrastructure that treats security as a default, not an add-on.
Encrypted storage
Uploaded reads and results are encrypted at rest and in transit.
Role-based access
Granular permissions control who can view, run, or manage jobs and data.
Audit logging
Every access and administrative action is recorded for review.
Configurable data retention
Available on the Clinical plan for teams with stricter data-handling requirements.
Simple, usage-based pricing
Start free. Upgrade when you need more throughput or faster turnaround.
Starter
2 WES analyses / month
- Standard variant report (PDF)
- ACMG classification
- Email support
- 12-hour turnaround
Research
15 WES analyses / month
- Everything in Starter
- Live chat support
- 8-hour turnaround
- Genome browser & custom gene panels
Clinical
60 WES analyses / month
- Everything in Research
- 2-4 hour turnaround
- Configurable data retention
- 99.9% uptime SLA
Frequently asked questions
Typical turnaround is 2-3 hours per sample on our standard infrastructure, from FASTQ upload to a completed, classified report - faster with a Clinical plan's priority queue.
Ready to analyze your Genome data?
Start with two free analysis Samples per month - no credit card required.