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QIAGEN CLC Genomics Workbench Premium

Focus on what really matters for your metagenomics, microbiome profiling, pathogen typing, genome-based outbreak or single-cell analysis research. Access all the bioinformatics tools you need to power your research. Readily integrated and streamlined NGS workflows combined with state-of-the art data interpretation and visualization enable you to shift your focus from data to discovery.

To trial QIAGEN CLC Genomics Workbench Premium, simply download QIAGEN CLC Genomics Workbench and extend its functionality by installing the plugin(s) of interest.

Your single toolkit for all NGS analysis applications

From data to discovery

Common challenges

Ever-growing sample volumes demand efficient bioinformatics. Yet a lack of well integrated analytics for microbial genomics and single cell analysis leaves researchers and organisations with the burden of integrating and maintaining all the required tools for bioinformatics, statistics and visualisations to power their research.

Integrated analytics for research continuity. All analytics come fully integrated into one scalable and enterprise-ready solution. Data and sample-metadata management is included.
Ready-to-use workflows We shift the focus from data to discovery by providing preconfigured workflows that streamline processing of raw NGS data. Researchers can focus on the interpretation of results, for example in the context of other samples or metadata.
Accurate performance Our algorithms are designed to save time and compute resources, and to be accessible to bioinformatics experts and non-bioinformaticians alike.

Extend your NGS capabilities with QIAGEN CLC Genomics Workbench Premium

QIAGEN CLC Genomics Workbench Premium expands upon QIAGEN CLC Genomics Workbench, the industry standard platform for bioinformatics computing.

Plugins and modules add a layer of specialized tools and workflows to QIAGEN CLC Genomics Workbench, creating a comprehensive solution for microbial genomics, metagenomics and single cell data analyses.

There is more: Experts in the field of microbial genomics are creating plugins for QIAGEN CLC Genomics Workbench Premium to bring additional tools and services to the user community.

Microbial and metagenomics

QIAGEN CLC Genomics Workbench Premium delivers tools and workflows for a broad range of bioinformatics needs for microbiome analysis, isolate characterization, functional metagenomics and antimicrobial resistance characterization.

Microbial profiling: Assemble and annotate high quality reference genomes for critical type strains, and manage your database of reference genomes. Learn more

Pathogen and outbreak analysis: Leverage whole genome analysis for epidemiological outbreak investigation. Accurately type and characterize microbial isolates. Monitor outbreaks and track pathogen transmission back to the source using modern phylogenetic tools. Learn more

Genome finishing: Short read lengths and repetitive genomic regions often result in fragmented de novo assemblies. To improve results and convert contigs into high quality assemblies a complex process referred to as genome finishing is needed. QIAGEN CLC Genome Finishing Module is an add-on to QIAGEN CLC Genomics Workbench Premium, designed to accelerate and simplify genome finishing, and make this process accessible to life scientists without deep understanding of bioinformatics. Learn more 

Single-cell analysis

QIAGEN CLC Single Cell Analysis Module enables analysis from raw FASTQ files to clusters of cells with annotated cell types and differentially expressed genes. It also lets you to visualize data from over a million cells at once. Additional functionality includes TCR-repertoire analysis, ATAC-seq support and RNA velocity analysis workflows. 

QIAGEN CLC Single Cell Analysis Module was developed based on the best-performing algorithms as assessed by recent independent benchmarking papers. The algorithms have been re-implemented to scale to the largest datasets and run on a wide range of hardware. 

Ultra-fast FASTQ to VCF processing

QIAGEN CLC LightSpeed Module provides tools and workflows for ultrafast FASTQ-to-VCF processing. Resulting VCFs can be uploaded to QIAGEN Clinical Insights (QCI) for interpretation. In our recent benchmark study, we showed that using our ultra-fast QIAGEN CLC LightSpeed technology our FASTQ to VCF hereditary workflow analyzes 34x human WGS samples in just 25 minutes for less than $1.

How can QIAGEN CLC Genomics Premium support your research goals?


In pharma


In agriculture and food


In public health and infectious disease

The role of bioinformatics – In Pharma

The bacteria in microbiomes are closely tied to their host’s health. They regulate our immune system and metabolism, they offer protection against pathogenic microbes, and produce essential vitamins.

A next generation of therapeutics that can modulate our microbiomes is emerging. Understanding how to shift microbiomes from dysbiosis (unhealthy state) to a healthy state is key to developing such therapies.

The role of bioinformatics: Discovery of microbes or molecules that can modulate microbiomes depends on software that enables the study of how taxonomic and functional profiles of microbiomes change in response to external factors.

Quality control of microbes that modulate microbiomes is another important task and requires a different type of genomics-based analytics: typing at strain- and gene level via whole genome analysis level becomes important.

Read more >

The role of bioinformatics – In Agriculture and Food

Microbiomes not only affect humans but are also agriculturally relevant. For instance, bacteria of the plant microbiome reside in soil, on leaves or inside the plant. New microbial seed supplements represent a sustainable and ecologically sound alternative to chemicals. Delivering select microbes to seeds, improves health and development throughout the plant life cycle, and optimizes yields.

Another important aspect is food safety. Food safety regulations aim at protecting consumers from foodborne illness, which involves tight surveillance from “farm to fork”.

Food safety means to protect consumers from foodborne illness and involves tight surveillance from “farm to fork”.

The role of bioinformatics: Developing seed supplements requires analytics that can link microbiome profiles to plant health and environmental factors.

Modern genomics and bioinformatics can help to quickly control food-borne contamination, which is key to ensuring food safety. After the detection and identification of pathogenic microbes, typing via whole genome analysis is the fastest, most accurate path to tracking a pathogen contamination back to the source. In addition, whole genome analysis can reveal the presence of genes involved in antimicrobial resistance.

Read more >

The role of bioinformatics – In Public Health & Infectious Disease

Infectious diseases impact public health on a global scale and come with a heavy personal burden for patients and a high economical burden. Detecting and controlling pathogen outbreaks early is key to protecting public health.

The role of bioinformatics: Modern bioinformatics can analyze and compare pathogen isolates at the level of whole genomes. Comparing genomic information of isolates in context of epidemiological metadata allows investigators to track a pathogen outbreak back to its source.

Whole genome analysis also serves the purpose of characterizing pathogens, for instance revealing genes contributing to antimicrobial resistance. Such information can be crucial for optimal outbreak control. Metagenomics enables early detection of pathogens in metagenomic samples.

Read more >

Let QIAGEN CLC Genomics support you in the classroom

Want to develop an NGS data analysis curriculum while advancing your own research goals? Check out the benefits of our teaching license package to QIAGEN CLC Genomics Workbench.

Start analyzing your microbial data now using a Sample to Insight workflow

Watch our webinar on using targeted whole viral genome sequencing to analyze and understand COVID-19. Discover the features of our latest QIAseq panel focused on sequencing the SARS-CoV-2 genome, and learn how QIAGEN CLC Genomics Workbench delivers in-depth sequence analyses and comparative genomic analysis.

The images on this webpage were taken prior to COVID-19.