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QIAGEN CLC Genomics Server

QIAGEN CLC Genomics Server is a multi-user, enterprise solution for high throughput sequencing analysis, designed for use on a central compute cluster or server. Along with a strong bioinformatics analysis offering, it can handle data volumes beyond the capacity of desktop systems and effectively manages the submission of many jobs via its own queuing system or through submission of jobs to a third party grid scheduler. It is designed to be easy and intuitive to use: a graphical interface for administration is included, and jobs can be submitted to the QIAGEN CLC Genomics Server through the user friendly, graphical menu system of the QIAGEN CLC Genomics Workbench or by using the command line.

Support your science

QIAGEN CLC Genomics Server supports import and export of major bioinformatics file formats, such as fastq, fasta, BAM, VCF, BED and others, and provides bioinformatics tools for the analysis of next generation sequencing data in many application areas. Plugins further expand its functionality, including supplying ready-to-use workflows for application areas such as biomedical analysismicrobial genomic analysis, and QIAseq panel data analysis.

Workflows on QIAGEN CLC Workbenches can be executed on the QIAGEN CLC Genomics Server, or they can be exported and installed directly on the QIAGEN CLC Genomics Server, allowing the same workflow, with the same settings, to be employed by multiple users.

Scale it and tailor it

QIAGEN CLC Genomics Server can be run on computer clusters either as a QIAGEN job node setup or by integrating with an existing grid setup via a DRMAA interface. We have verified our grid integration on the following systems:

  • SLURM 16.05.2
  • UNIVA 8.4.1
  • LSF 9.1.1 and 10.1
  • PBS Pro 14.2.1

Data folders mounted from a central data storage system and attached to the compute cluster or server are accessible to via the server or client interfaces. Group-level access control can be applied via LDAP, Active Directory or the built-in access system, allowing administrators to fine tune who has access to different aspects of the server, such as read or write permissions on particular data folders, the ability to run certain tasks, access to particular grid queues, and so on.

The QIAGEN CLC Genomics Server’s External Applications functionality allows the integration of non-interactive, command line software, such as many open source bioinformatics tools, such that they can be launched via the graphical menu system of the QIAGEN CLC Genomics Workbench, independently or as part of a workflow, or launched using the CLC Server Command Line Tools.

In addition, a flexible plugin system utilized by the API and our Software Development Kit makes it possible to tightly integrate your own algorithms directly into the software, making them available to launch via the client software of the QIAGEN CLC Genomics Server.

Further customized functionality is available through the QIAGEN CLC Informatics Custom Solutions team, who provide a comprehensive suite of consulting, development, training, and other professional services.

One unified environment

Using external applications with
Whole Exome Sequencing Benchmark
Using CLC Command Line Tools

System requirements

The QIAGEN CLC Genomics Server system requirements are available on our general system requirements page and also in the user manual.

QIAGEN CLC Genomics Server job nodes and grid nodes must run on the same type of operating system as the master node.


Analyses on the QIAGEN CLC Genomics Server can be initiated using a QIAGEN CLC Genomics Workbench or the CLC Server Command Line Tools.

Latest improvements

We frequently release updates and improvements such as new functionalities, bug fixes or plugins. A full list of recent changes are listed on the latest improvements page.

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