Introducing CAS Pathogen, Celemics’ New Pathogen Analysis Platform
Sequencing Has Become Easier, But Analysis Remains Complex
The biggest bottleneck in pathogen NGS workflows is no longer sequencing itself—it is what comes afterward. While advances in sequencing technologies and target enrichment methods have made generating pathogen genomic data easier than ever, transforming that data into actionable insights remains a significant challenge for many laboratories and public health organizations.
Even after sequencing is complete, researchers must perform quality control, alignment, variant calling, consensus sequence generation, data visualization, and reporting. These processes often require specialized bioinformatics expertise and dedicated computational infrastructure, creating a barrier to broader adoption of pathogen genomics.
To address this challenge, Celemics introduces CAS Pathogen, a cloud-based pathogen analysis platform built on CAS (Celemics Analysis Service). With a single FASTQ upload, CAS Pathogen automatically performs QC, alignment, variant calling, and consensus sequence generation, delivering results through intuitive visualizations and comprehensive PDF reports.
Why a Pathogen Analysis Platform Matters
Since the COVID-19 pandemic, pathogen surveillance has expanded far beyond specialized reference laboratories. Public health agencies, hospitals, and research institutions worldwide are increasingly adopting genomic approaches to identify and monitor infectious diseases.
Demand continues to grow for rapid pathogen identification across a variety of clinical syndromes, including respiratory infections, hemorrhagic fever, and rash-associated febrile illnesses. NGS-based Target Enrichment technologies provide a powerful solution by enabling simultaneous detection of viruses, bacteria, and fungi while supporting genomic-level monitoring of emerging variants.
However, the primary challenge is no longer sequencing—it is data analysis. CAS Pathogen was developed to simplify this workflow and lower the barrier to pathogen genomics adoption.
How should raw FASTQ files be processed?
Do researchers need to build pipelines for QC, alignment, variant calling, and consensus generation?
How can results be presented in a format that clinicians, epidemiologists, and policymakers can easily understand?
CAS Pathogen: Automating the Journey from FASTQ to Report
- Fully Automated Analysis Pipeline
CAS Pathogen automates the entire workflow from quality control and alignment to variant calling and consensus sequence generation.
Users simply upload FASTQ files and receive standardized results without building custom pipelines or running command-line scripts.
- Intuitive Data Visualization
CAS Pathogen provides interactive visualizations of coverage depth, read distribution, and variant analysis results.
The platform is designed to make complex genomic information accessible even to users without specialized bioinformatics training, enabling faster and more confident decision-making.
- Comprehensive Report Generation
Analysis results are automatically compiled into detailed PDF reports. These reports are suitable for research documentation, public health surveillance programs, scientific publications, and epidemiological investigations, minimizing the need for additional data processing or formatting.
- Cloud-Based Accessibility
CAS Pathogen requires no local installation or dedicated high-performance computing infrastructure. Researchers can securely access the platform from anywhere through a standard web browser, making pathogen analysis accessible regardless of laboratory size or available resources.
Sample to Insight: An End-to-End Workflow
While CAS Pathogen functions as a powerful standalone analysis platform, its value is maximized when integrated with Celemics Target Enrichment solutions. By connecting reagents, sequencing, and bioinformatics into a pre-validated workflow, Celemics simplifies the journey from sample to actionable insight.
- Hybridization Capture Workflow
Hybridization Capture is well suited for broad pathogen discovery and applications requiring uniform whole-genome coverage across large genomic regions.
- Amplicon Sequencing Workflow
Amplicon-based enrichment provides rapid analysis of low-input samples and efficient high-throughput sequencing of predefined targets.
- A Unified Analysis Experience Regardless of Workflow
Regardless of the Target Enrichment strategy selected, downstream analysis is performed through the same CAS Pathogen environment. Each step is standardized using validated Celemics reagents and protocols, while CAS Pathogen manages the final analysis process. This integrated workflow significantly reduces hands-on time from sample receipt to final report generation.
Pre-Integrated with Syndrome-Driven Panels
CAS Pathogen is pre-integrated with Celemics syndrome-driven pathogen panels. Once a panel is selected, optimized reference databases and variant analysis workflows are automatically applied, simplifying analysis and ensuring consistency across studies.
Syndromic Panels — Symptom-Driven Multi-Pathogen Detection
These panels begin with clinical presentation and enable simultaneous detection of multiple pathogens associated with specific symptoms.
Infectious Respiratory Syndrome Panel
Designed for the detection of pathogens associated with respiratory infections.- Hemorrhagic Fever Syndrome Panel
Targets pathogens responsible for hemorrhagic fever syndromes.
- Rash with Fever Syndrome Panel
Supports detection of pathogens associated with rash and febrile illness.
Targeted Panels — Deep Analysis of Specific Pathogen Groups
These panels provide high-resolution sequencing information for selected pathogen groups when more focused analysis is required.
Pathogen Amplicon Panel
Supports amplicon sequencing of major respiratory viruses, including Influenza A/B, RSV, and HMPV.- Biological Agent Detection Panel
Designed for surveillance of biological threat agents and biodefense-related applications.
Compatible with Major NGS Platforms
CAS Pathogen is platform agnostic and supports sequencing data generated from major NGS systems, including Illumina, Thermo Fisher (Ion Torrent), and MGI. This flexibility allows laboratories to standardize their analysis workflow without changing their existing sequencing infrastructure.
Standardizing Pathogen Genomics Workflows for Surveillance and Research
The value of pathogen genomics extends beyond generating sequencing data. Equally important is the ability to interpret data quickly, consistently, and reproducibly to support real-world decision-making.
In public health surveillance and outbreak investigations, differences in analysis pipelines can make it difficult to compare results across laboratories and institutions.
CAS Pathogen helps standardize the entire workflow—from FASTQ upload to analysis, visualization, and reporting—making pathogen genomics more accessible while supporting efficient infectious disease research and surveillance programs.
[Who Can Benefit from CAS Pathogen?]
- Public health laboratories and infectious disease surveillance organizations
- Hospital infectious disease and clinical pathology departments
- Veterinary, environmental, and food safety researchers
- One Health research programs
- Laboratories with limited bioinformatics resources
See What the Output Looks Like
The value of pathogen genomics is not only in generating sequencing data, but also in presenting those results in a format that can be easily interpreted and shared. CAS Pathogen automatically visualizes coverage depth, read distribution, variant analysis results, and consensus sequence information while generating comprehensive PDF reports. Explore a sample analysis result page to see how sequencing data is transformed into actionable insights through the CAS Pathogen platform.
Explore CAS Pathogen
CAS Pathogen provides an automated pathogen analysis environment covering QC, alignment, variant analysis, consensus sequence generation, visualization, and reporting from a single FASTQ upload.
Standardize your pathogen genomics workflow for public health surveillance, clinical research, and One Health applications.
