ATGCFLOW
Platform Features

Eight stages, one pipeline — nothing stitched together by hand.

Quality control through clinical reporting, run as a single orchestrated workflow — high-accuracy variant calling, automated ACMG/AMP interpretation, and a report your team can sign off on. Research use only.

Quality Control
Variant Calling
ACMG Classification
Gene Panels
Genome Browser
Clinical Reports
API Access
Batch Processing
Analysis Pipeline

The eight stages, start to finish.

From raw FASTQ files to clinical reports in hours, not days

STEP 01

Quality Control

Pre-processing and quality assessment

STEP 02

Read Alignment

Mapping reads to GRCh38 reference

STEP 03

Variant Calling

SNV and indel detection

STEP 04

Annotation

Multi-source functional annotation

STEP 05

Classification

ACMG/AMP criteria application

STEP 06

Filtering

Gene panel and quality filters

STEP 07

Visualization

Interactive genome browser

STEP 08

Reporting

Clinical report generation

Average Turnaround Time
2-4 hours

Quality Control & Preprocessing

Comprehensive quality assessment ensures only high-confidence data enters the analysis pipeline

Key Features

Per-base quality score analysis
Adapter sequence trimming
Read length distribution
GC content assessment
Duplicate read identification
Contamination screening

Technical Details

FASTQ format validationPhred quality score thresholdsAutomatic quality filteringDetailed QC metrics reports

Alignment & Variant Calling

State-of-the-art algorithms for accurate read mapping and variant detection

Key Features

Alignment to GRCh38 reference genome
Base quality score recalibration
Indel realignment
Duplicate marking
SNV and indel calling
Copy number variation detection

Technical Details

Industry-standard short-read alignmentGermline variant callingMinimum mapping quality: Q20Target coverage: 100x mean

Multi-Source Annotation

Comprehensive variant annotation from 20+ curated databases

Key Features

Population frequency data
Clinical significance annotations
Functional impact predictions
Protein domain annotations
Gene constraint metrics
Splice site predictions

Technical Details

Comprehensive functional annotation engineCurated gene and transcript modelsVariant identifier cross-referencesCancer-associated mutation references

ACMG Classification Engine

Automated variant classification following ACMG/AMP 2015 guidelines

Key Features

Evidence-based pathogenicity scoring
PVS, PS, PM, PP criteria evaluation
BA, BS, BP criteria assessment
Automated classification (P/LP/VUS/LB/B)
Supporting evidence documentation
Conflicting interpretation resolution

Technical Details

Independent classification cross-check28 evidence criteria evaluationExpert-panel-aligned classification guidelinesManual override capability

Gene Panel Filtering

Focus analysis on clinically relevant genes for your specific indication

Key Features

500+ curated clinical gene panels
Custom gene list upload
Inheritance pattern filtering
Frequency-based filtering
Quality threshold filtering

Technical Details

Curated gene panel sourcesDisease-gene association dataFlexible filter combinations

Interactive Genome Browser

Interactive visualization for detailed variant inspection and validation

Key Features

Real-time BAM/VCF viewing
Coverage depth visualization
Allele fraction analysis
Splice junction display
Multi-sample comparison
Bookmark and annotation

Technical Details

Real-time genome visualization engineWebGL-accelerated renderingRemote file streamingCustom track support

Interactive Visualizations

Publication-ready charts and graphs for data exploration

Key Features

Variant distribution plots
Coverage uniformity graphs
Allele frequency histograms
Quality metrics dashboards
Comparison visualizations
Exportable vector graphics

Technical Details

D3.js and Plotly chartsSVG/PNG exportResponsive designInteractive tooltips

Report Generation

Professional clinical reports with comprehensive variant summaries

Key Features

Structured clinical reports
Variant summary tables
ACMG classification evidence
Gene-disease associations
Literature references
Quality metrics summary

Technical Details

PDF/Excel export formatsCustomizable templatesHGVS nomenclatureStructured audit trail
Technical Specifications

Platform capabilities, plainly stated.

Production-ready infrastructure for high-throughput genomic analysis

Input Formats

  • FASTQ (paired-end)
  • BAM/CRAM files
  • VCF files
  • BED gene panels

Output Formats

  • Annotated VCF
  • Excel reports
  • PDF clinical reports
  • JSON API data

Reference Genome

  • GRCh38/hg38
  • Curated transcript models
  • Gene annotation reference
  • 50+ GB databases

Compute Requirements

  • 16+ CPU cores
  • 64 GB RAM
  • 500 GB storage
  • GPU acceleration

Integration Options

  • RESTful API
  • CLI interface
  • Web dashboard
  • Batch processing

Quality Standards

  • Research Use Only (RUO)
  • Encrypted storage & transit
  • Role-based access control
  • Audit logging

Ready to see it running on your own data?

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