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CLC Genomics Server
A flexible enterprise level infrastructure and analysis backbone for next generation sequencing data analysis.
Overview
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.
Get a quick overview of our enterprise platform
Many scientists are experiencing increased size and complexity in the NGS datasets they have to analyze, which effectively makes data analysis a bottleneck in some workflows…
Some of the available bioinformatics analyses
- Read mapping of Sanger and high-throughput sequencing data
- De novo assembly of Sanger and high-throughput sequencing data
- Variant detection on whole genomes of any size
- Detection of structural variations on whole genomes of any size
- Resequencing tools
- ChIP-seq analysis
- RNA-seq analysis
- Small RNA analysis
- BLAST
- Automation of analysis workflows
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:
CLC Genomics Server version 4.5 made it possible to design and maintain workflows with a graphical user interface.
For more information, read the user manual and the product sheet.
See the latest improvements of CLC Genomics Server
Features
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.
Available bioinformatics analyses
- Read mapping of Sanger and high-throughput sequencing data
- De novo assembly of Sanger and high-throughput sequencing data
- Automation of analysis workflows
- SNP detection on whole genomes of any size
- Detection of structural variations on whole genomes of any size
- ChIP-seq analysis
- RNA-seq analysis
- Small RNA analysis
- BLAST
- Probabilistic variant detection
- Annotate small RNA
More…
- Trim sequences
- Secondary peak calling
- Import tools for high throughput sequencing data
- Extract and count small RNA
- Process tagged sequences
- Create detailed mapping report
- External applications framework (integration with 3rd party programs on the server)
- Velvet, integrated through external applications framework
- Bowtie, integrated through external applications framework
- Additional plugins with specialized analyses
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
- FASTQ
- RNAML
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.
Options
The Client Layer
The 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.
CLC Genomics Workbench
The CLC Genomics Workbench is the premium and award-winning client for our Enterprise Solutions. It gives the user full control of all bioinformatics analyses on the CLC Genomics Server in terms of service-invocation and monitoring. Furthermore it is possible to seamlessly view your results even with limited network-load, due to our advanced handling of genome sized sequences on the server-side.
CLC Server Command Line Tools
With a toolbox of Command Line Tools for the server, the advanced user can incorporate server-access in scripts, integrations etc. Furthermore, it is possible to inspect and invoke all services and upload/download any data in virtually any format.
Web interface
The thin client access to the Genomics Server is a powerful administration interface to the solution. It is possible to do more user-oriented things like browsing data, upload/download data, access/edit meta-data on data and do data-queries.
Flexible
Customization
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.
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.
Flexible
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.
The File System
When using this option you never have to worry about local data, different versions of data or disappearing data.
The simplest way to manage your data on the server-side is to attach a File System to the CLC Genomics Server. This serves as a central data store that is accessible and manageable from anywhere in your organization.
It is also possible to make use of advanced data-mining features to find exactly the data you need for your project.
The solution has very flexible built-in tools for restricting access to different user-groups within your organization.
CLC Bioinformatics Database
For maximum flexibility, security and scalability you can choose to use CLC Bioinformatics Database as Data Management system for the solution with all the same advantages of central storage as using a central File System.
The CLC Bioinformatics Database in combination with the CLC Genomics Server make your Data Management Layer highly scalable, by using the built-in tools of your favorite Database Management System (DBMS). Comes with built-in support for the most popular DBMS like Oracle, MySQL, MS SQL Server and PostgreSQL.
The solution has very flexible built-in tools for restricting access to different user-groups within your organization.
Custom Database Schemas
Using our APIs for Data Management you can integrate your own custom Database Schemas in the solution. We have several customers who can present great success with this.
The integration efforts are usually done by the customer, by CLC bio or as a combination. If you have more interest in this, we suggest you have a look at our pages regarding CLC Developer Kit or CLC Consulting Solutions
Scalability
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 DRMA support
Besides the internal job scheduling system, third party schedulers with an available DRMAA library can be used. Currently the supported job scheduling systems for CLC Genomics Server are:
- Oracle Grid Engine
- Open Grid Scheduler/Former Sun Grid Engine
- PBS Pro by Altair
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.
