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CLC Genomics Server

A flexible enterprise level infrastructure and analysis backbone for next generation sequencing data analysis.

Genomics Server


Centralized Bioinformatics Analyses

CLC Genomics Server is an advanced high-throughput sequencing focused three-tier solution offering secure, powerful, and flexible bioinformatics computing on a server-architecture located centrally in your organization.

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Some of the available bioinformatics analyses

See the full list and read more about bioinformatics analyses .

Good reasons to invest in a CLC Genomics Server

  • Compute resource management: Central execution platform with flexible queuing system, designed for your bioinformatics analysis and services.
  • Flexible: Based on a 3 tier system architecture to offer maximum security and intractability within fields of biology and bioinformatic computing.
  • Premium system-clients: Offers maximum client-flexibility with support for our user-friendly and award winning CLC Genomics Workbench as a premium system-client.
  • Customizable: Highly customizable on both client-side and server-side using our SDK or various command line tools.
  • Scalable: Highly scalable with support for CLC Server Nodes.
  • Advanced data I/O: Offers an advanced and customizable data-import/export framework, that also can be used for data conversion.
  • Shared data: Store your data on central storage. This can be either a file system, the CLC Bioinformatics Database or on a custom designed database scheme.

Design custom workflows to support your science

With CLC Command Line Tools of CLC Genomics Server, it is possible to define your own workflows. This is done in terms of scripts that interact with the CLC Command Line Tools. With the solution a sample script workflow is given, that imports NGS reads, maps the reads to a reference, followed by SNP and DIP detection:

For more information, read the user manual and the product sheet.

See the latest improvements of CLC Genomics Server


Bioinformatics analysis

CLC Genomics Server Core gives you a unique and stable software architecture core, that makes it possible to apply a range of bioinformatics analysis-services on your high-throughput sequencing data. The server administrators can furthermore decide if certain groups should not be allowed to run certain analyses. This can be controlled also for each external application configuration.

Supported data formats

  • Phylip Alignments (.phy)
  • Macromolecular Crystallographic Info File (.cif)
  • Clustal Alignment (.aln)
  • Embl (.emb)
  • FASTA (.fsa)
  • Vector NTI (.ma4, .pa4, oa4)
  • Gene Construction Kit File (.gcc)
  • Blast Db (.phr, .pal, .nhr, .nal)
  • GCG Sequence (.gcg)
  • GenBank (.gbk)
  • Lasergene sequence (.pro, .seq)
  • GCG Alignment (.msf)
  • Newick (.nwk, .newick)
  • Protein Data Bank (.pdb)
  • PIR (.pir)
  • CLC (.clc)
  • Staden Sequence (.sdn)
  • DNA Strider files (.str)
  • SwissProt (.swp)
  • Plain Text (.txt)
  • Trace files (.abi, .ab1, .scf, .phd)
  • Zip files (.zip)
  • Excel
  • col
  • CT File

High-throughput sequencing formats

  • Roche 454
  • Illumina
  • SOLiD
  • Sanger
  • SAM/BAM mapping files
  • Tabular mapping

All bioinformatics analyses can be accessed from CLC Genomic Workbench or from a command line interface. Quickly get an overview of our enterprise platform! Read the manual for CLC Genomics Workbench for more info.


Client layer options

CLC Genomics Server comes with three client options

Common for all clients to the CLC Genomics Server is that they are built on our service oriented SOAP web-services. This gives a full choice on the client-side of the system, including option to design your own client.

All connections from clients (either Workbench, Command Line Tools or the web interface) to the server are of course secured through SSL.



Right from the start CLC Genomics Server has been designed for advanced customization. This fact makes it one of the most flexible bioinformatics platforms in the world.

The key-point is that the customer has the vision, CLC bio has the platform, and the combination of these drives a successful solution implementation. There are several approaches and options for customization to choose from.

Plugin Development

CLC Genomics Server comes with an advanced API, that makes it possible to design/develop/deploy your own bioinformatics analyses directly on the system and making them available to the user through any of the platform’s client options.

Examples of relevant plugins could be deployment of proprietary algorithms or integration with existing IT-infrastructure.

More information can be found at our SDK section and our dedicated web-site CLC Developer Connection. It is free to sign up.

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Integration of External Applications

With the built-in support for External Command Line Applications, it is possible to deploy External Applications seamless into the CLC Genomics Server without doing any programming. The result is bioinformatics analysis that is available for the end-user, with a graphical user-interface for service-invocation and viewing of results. The purpose of this is to make a platform for bioinformaticians, so they can concentrate on the creative side of their job, and thereby create more value for your organization.

Furthermore this has great advantages to biologists and bio-medical experts, since advanced tools and services can be available to them, with a nice user-friendly user-interface in terms of the CLC Genomics Workbench. The simple goal is to enhance productivity in all parts of your organization.

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Data Management

The CLC Genomics Server comes with a flexible data management solution, which is based on years of experience with large amounts of Genomics Data. This ensures a smooth handling and viewing of genomics data across networks, based on user actions. This means that only the data the user works on are transferred to and from the clients and most likely never whole genome data sets.

The Data Management architecture has very flexible built-in tools for restricting access to different user-groups within your organization. The CLC Genomics Server solution offers 3 very flexible solutions to manage your bioinformatics data.


Job Node Support

With the built-in Job Node Support of the CLC Genomics Server, it is possible to attach an array of real or virtualized computers to the solution. This array of computers will serve as the core execution points of your bioinformatic services based on queue prioritization. It is possible to configure each Job Node to only being execution-point to certain types of tasks.

External grid integration

CLC Server jobs can be sent from a master server out to grid nodes, where a grid scheduling system is used to handle job scheduling and submission. CLC bio supports the third party scheduling systems OGE, PBS Pro and IBM Platform LSF*.

*Tested versions are:
OGE 6.2u6
PBS Pro is 11.0
LSF 8.3 and 9.1

More details about external grid integration

Latest improvements

We frequently release updates and improvements such as bug fixes, new features or plugins. To get a complete overview, please visit our latest improvements page.


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For more information and a trial, please contact us.

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