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A comprehensive set of NGS and 'omics data analysis tools with flexible access, from a laptop to a local server to the cloud

Powerful bioinformatics tools to scale your research analyses

Gain clearer insights into your complex sequencing, NGS or ‘omics data with our comprehensive bioinformatics software for all your genomics, transcriptomics and epigenomics analysis needs. This easy-to-use bioinformatics software enables you to develop workflows and visualizations for any sequence-based analysis.

Explore our NGS and ‘omics data analysis tools for:

  • Bioinformatics workflows 
  • Microbial genomics

  • Biomedical genomics
  • Single-cell analysis
  • Ultra-fast FASTQ to VCF processing
  • Enterprise solutions

QIAGEN CLC software for bioinformatics, NGS and 'omics data analysis: Get the features that meet your needs

QIAGEN CLC Main Workbench:
For basic sequencing analysis
QIAGEN CLC Genomics Workbench: For NGS sequencing analysis
QIAGEN CLC Genomics Workbench Premium: Full-featured solution
  • Primer design
  • Multiple sequence alignment tools
  • Phylogenic analysis tools
  • Sanger sequencing analysis
  • Molecular cloning, including Gibson cloning
  • Microarray expression analysis
  • 3D molecular modeling
  • Support most sequence formats, including Vector NTI
  • Workflow editor
  • Whole genome alignment

Includes all the features of the QIAGEN CLC Main Workbench, plus:

  • De novo assembly of NGS reads from any platform
  • Supports all organisms 
  • Resequencing analysis and variant calling
  • Long read analysis (PacBio, Oxford Nanopore)
  • RNA-seq (including miRNA and lncRNA), ChIPseq, DNA methylation
  • Biomedical genomics analyses, including TMB, CNV, LoH and HRD immune repertoire typing (TCR and BCR)
  • Haplotype calling
  • QIAseq panel analysis workflows

Includes all the features of the QIAGEN CLC Genomics Workbench, plus:

  • Ultra-fast FASTQ to VCF pipelines
  • Single-cell analysis
  • Microbial typing
  • Antimicrobial resistance
  • Metagenomics characterization
  • Genome finishing

QIAGEN CLC enterprise solutions: For organization-wide and command line access​

Scale your NGS: From single-user to enterprise-friendly data analysis, our NGS enterprise solutions for whole genome data analyses are scalable and support multiple users in an intuitive way.

Our QIAGEN CLC enterprise solutions include:

  • QIAGEN CLC Genomics Server
  • User management and administration
  • QIAGEN CLC command line tools
  • QIAGEN CLC Genomics Cloud Module


Any species, any platform, any workflow: The all-purpose power tool for NGS data analysis

• Template workflows: Over a dozen pre-built, flexible workflows to accelerate analysis of your cancer and hereditary disease data. Build your own customized analysis workflows for a wide range of both DNA and RNA sequencing data

• Intuitive interface: Interactive visualization of your data linked to a best-in-class track viewer

• Visualize and share results with the built-in Genome Viewer

• Platform independent: Supports common sequencing platforms (Illumina, Ion Torrent, PacBio, Oxford Nanopore and BGI/MGI) and runs on most operating systems

• Enterprise ready: Support multiple users in an intuitive way, with high-throughput analysis and automation

Tools in the QIAGEN CLC Genomics portfolio:

Bioinformatics workflows

User-friendly bioinformatics software solutions enable a comprehensive analysis of your NGS data. For basic sequencing analysis, QIAGEN CLC Main Workbench offers core workflows such as DNA and gene expression, primer design, molecular cloning, phylogenetic analyses and data management. QIAGEN CLC Genomics Workbench provides advanced NGS workflows for de novo assembly of whole genomes and transcriptomes, resequencing analysis (WGS, WES and targeted panel support), variant calling, RNA-seq, ChIP-seq and DNA methylation (bisulfite sequencing analysis).

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Microbial genomics

Uncover critical correlations among microbiota, metagenome and host. Easily understand complex metagenomic data through tools and streamlined analysis workflows for gene finding, annotation, taxonomic and functional microbiome analysis. Our solutions for microbial genomics include tools and workflows for a broad range of bioinformatics needs for microbiome analysis, isolate characterization, functional metagenomics, pathogenicity, strain typing and resistance identification.

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Biomedical genomics

Empower your biomedical analyses with prebuilt workflows for human, mouse and rat genomics, including support for QIAseq UMI-based NGS library preparation kits and panels. Content includes hereditary disease workflows, oncology somatic mutation detection workflows for cancer FFPE or liquid biopsy (single sample or matched tumor-normal) samples, sensitive detection of SNPs, MNVs, indels, tandem repeats, structural variants, fusion genes and CNVs.

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Enterprise solutions

Grow and scale your NGS capabilities beyond the number of available desktops. Our enterprise NGS solution can be deployed on a local server that manages the submission of many jobs via its own queuing system or through the submission of jobs to a third-party grid scheduler. QIAGEN CLC Cloud Module makes bioinformatics analysis scalable and accessible to anyone involved in the analysis of NGS data. It lets you build your workflows locally in QIAGEN CLC Genomics Workbench and then deploy them on Amazon Web Services (AWS) in minutes.

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Plugins and Modules

With many plugins and modules, these feature-rich extensions are seamlessly integrated and provide advanced tools and workflows to meet your specific analysis needs. Some of the most popular plugins include:

Explore the full list of available plugins:

Interested in QIAGEN CLC Genomics software?

Request a consultation with one of our bioinformatics specialists to discuss your specific research requirements.


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