AWS-Native · One Click

RNA-seq Pipeline

Drop your FASTQ files in S3, click run, and get a comprehensive QC report with processed counts and TPMs — in hours, not days.

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From Upload to Insights in Three Steps

No workflow configuration. No YAML manifests. No command-line expertise. Just your data, one click, and results.

flowchart LR A["① Upload Data
Drop FASTQ files
into your S3 bucket"] --> B["② One Click
Pipeline auto-discovers
samples, runs end-to-end
on AWS HealthOmics"] B --> C["③ Download Results
QC HTML Report
Count Matrices
TPM Expression Matrix"] B -.->|optional| D["Agent Mendel
DE Analysis
Pathway Scoring
AI Interpretation Report"] style A fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style B fill:#b5e8e5,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style C fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style D fill:#ffffff,stroke:#81d8d0,stroke-width:2px,stroke-dasharray:5,color:#0a5c5a

GenoSapiens RNA-seq Pipeline

A validated, AWS-native Nextflow pipeline built on AWS HealthOmics — benchmarked against Seq-QC community standards.

flowchart LR A["FASTQ
Raw Reads"] --> B["FastQC
Quality Control"] B --> C["HISAT2
Alignment"] C --> D["featureCounts
Gene Quantification"] D --> E["Merge Matrices
Aggregate Samples"] E --> F["MultiQC
HTML QC Report"] E --> G["Counts + TPMs
Expression Matrices"] E -.->|optional| H["Agent Mendel
DE + Pathway + AI"] H --> I["Analysis Report
AI-Powered HTML"] style A fill:#e8f7f6,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style B fill:#d1efed,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style C fill:#b5e8e5,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style D fill:#b5e8e5,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style E fill:#81d8d0,stroke:#0abab5,stroke-width:2px,color:#0a3d3d style F fill:#e8f7f6,stroke:#0a5c5a,stroke-width:2px,color:#0a3d3d style G fill:#e8f7f6,stroke:#0a5c5a,stroke-width:2px,color:#0a3d3d style H fill:#ffffff,stroke:#81d8d0,stroke-width:2px,stroke-dasharray:5,color:#0a5c5a style I fill:#ffffff,stroke:#81d8d0,stroke-width:2px,stroke-dasharray:5,color:#0a5c5a

What You Get

Every run delivers a complete, ready-to-use output bundle.

Output Format Description
QC Report HTML MultiQC summary — alignment rates, read quality, coverage
Raw Count Matrix TSV Gene-level counts across all samples
TPM Matrix TSV Transcripts-per-million normalized expression
FPKM Matrix TSV FPKM-normalized expression values
Agent Mendel Report optional HTML AI-powered DE analysis, pathway scoring, interpretation

Ready to Accelerate Your RNA-seq Analysis?

Request access. Drop your data, click run, and get results in hours.

Request Access