This page lists the requirements of all CLC software products, plugins and special use cases. Requirements for Biomedical Genomics Analysis plugin, CLC Single Cell Analysis Module, CLC Microbial Genomics Module vary and are listed separately below, as are special use case requirements for 3D Molecule Viewer, read mapping and de novo assembly. Please note that analysing data generated with QIAseq panels using the Biomedical Genomics Analysis require 16 GB RAM, 24 GB recommended.
* Standard requirements without use of functionality in plugins
Memory and CPU settings for mapping reads
For mapping to the human genome ( 3.2 gigabases), or genomes of a similar size, 16 GB RAM is required. Smaller systems can be used when mapping to small genomes.
Larger amounts of memory can help the overall speed of the analysis when working with large datasets, but little gain is expected above about 32 GB of RAM.
Increasing the number of CPUs can decrease the time a read mapping takes, however, performance gain is expected to be limited above approximately 40 threads.
System requirements for 3D viewers
A graphics card that supports OpenGL 2.0.
Note: 3D rendering is only supported when the CLC Genomics Workbench is installed on the same machine the viewer is opened on. Indirect rendering (such as X11 forwarding through ssh), remote desktop connection/VNC, and running in virtual machines is not supported.
System requirements for de novo assembly
De novo assembly may need more memory than stated above - this depends both on the number of reads, error profile and the complexity and size of the genome. See http://resources.qiagenbioinformatics.com/white-papers/White_paper_on_de_novo_assembly_4.pdf for examples of the memory usage of various data sets.
Requirements for CLC data locations are provided in Adding locations.
Working on large systems
When using large systems (>64 cores), a CLC Genomics Server with job nodes running on virtual machines provides potential to use more of the compute capacity in a controlled manner than a CLC Genomics Workbench. Jobs submitted to a CLC Genomics Server job node setup can be run in parallel, with appropriate CPU limits configurable for each node.
If you choose to run the CLC Genomics Workbench on a system with more than 64 cores, you will need a network license.
Biomedical Genomics Analysis plugin The system requirements of Biomedical Genomics Analysis are the same as those for the CLC Genomics Workbench apart from the following:
Special requirements for QIAseq analysis The following use cases have specific system requirements
CLC LightSpeed Module The system requirements of the CLC LightSpeed Module are the same as those for the CLC Genomics Workbench, apart from the following:
CLC Single Cell Analysis Module The system requirements of CLC Single Cell Analysis Module are the same as those for the CLC Genomics Workbench, apart from the following:
Most tools can be run on modest hardware such as a laptop, especially when the number of cells is under 50,000. Special requirements for mapping reads For mapping reads to references, we recommend using a CLC Genomics Server (see requirements below). Although a laptop with 16 GB of RAM can be used, the large number of reads are likely to lead to long runtimes when there are more than 1000 cells. Long Read Support plugin The system requirements of the Long Read Support plugin are the same as those for the CLC Genomics Workbench, apart from the following:
Special requirements when assembling PacBio HiFi reads with De Novo Assemble Long Reads At least 32 GB RAM is recommended for running the De Novo Assemble Long Reads tool with PacBio HiFi reads. Special requirements for Correct Reads and Polish with Reads Correct Reads and Polish with Reads use Racon [Vaser et al., 2017]. See the manual for details. CLC Microbial Genomics Module The system requirements of CLC Microbial Genomics Module are the same as those for CLC Genomics Workbench, apart from the following:
Special requirements for the MLST Scheme tools The system requirements for the MLST Scheme tools depend on the size of the MLST schemes (both the number of alleles and the number of sequence types). A laptop with 16GB of memory is normally sufficient for 7-gene schemes or cgMLST schemes based on a moderate number of isolates. Typing or constructing larger schemes may require more memory, and in general, we recommend at least 64GB of memory when working with cg/wgMLST schemes based on more than 100 isolates. Special requirements for the Taxonomic Profiler The quality performance of the Taxonomic Profiler depends on the reference database used – the more complete a database, the better the quality. However, running the Taxonomic Profiler with a given database size will require at least the same amount of memory. For example, running with a 14 GB database requires at least 16 GB of RAM, and running with a 56 GB database requires a minimum of 64 GB RAM. When creating your reference database with the Download Microbial Reference Database tool, you will get a warning about the memory requirements needed for running the Taxonomic Profiler with this database. Special requirements for De Novo Assemble Metagenome It is recommended to have at least 16 GB RAM when running the De Novo Assemble Metagenome. Special requirements for OTU Clustering The memory requirement of Reference based OTU clustering depends on the size of the reference database used; more and longer sequences require more run time and memory. Newer version of common choices (e.g. the full SILVA SSU database) are likely to be too large for a 16 GB machine. Instead we recommend using clustered databases (e.g. the SILVA SSU 99% database) and/or otherwise filtering and subsetting the database, to minimize its size. Special requirements for Classify Long Read Amplicons The memory requirement for Classify Long Read Amplicons depends on both sample size and the size of reference database. See the manual for details.
System requirements for 3D viewers A graphics card that supports OpenGL 2.0. Note: 3D rendering is only supported when the CLC Main Workbench is installed on the same machine the viewer is opened on. Indirect rendering (such as X11 forwarding through ssh), remote desktop connection/VNC, and running in virtual machines is not supported.
* Standard requirements without the use of functionality in plugins. For compute-intensive operations used by several plugins and modules, the recommended number of cores is 32. Server system
Hardware requirements
Working on large systems When using large systems (>64 cores), a CLC Genomics Server with job nodes running on virtual machines provides potential to use more of the compute capacity than a single CLC Genomics Server. Jobs submitted to a CLC Genomics Server job node setup can be run in parallel, with appropriate CPU limits configurable for each node.
The CLC Network License Manager does not require much processing power and only consumes a few megabytes of memory. This means that if you are putting together a dedicated server specifically for running the license manager, a modestly powered system equipped with a high number of redundant components will probably be a better investment than a system which is faster, has more memory, etc. The system requirements for the CLC Network License Manager are:
The list of systems above has been derived from the LM-X supported system list: https://docs.x-formation.com/display/LMX/Supported+platforms and systems we have tested on. The CLC Network License Manager will likely work on other Windows, Linux and macOS systems, but we cannot guarantee this.
The QIAGEN CLC Workbenches, CLC Command Line Tools, CLC Genomics Server and the CLC Network License Manager are built using Java technology. The QIAGEN CLC software includes a JRE (Java Runtime Environment) necessary to execute the software, independent of the operating system (Windows, Mac OS X or Linux). This JRE will not interfere with existing JRE’s on your computer and will only be used to run the QIAGEN CLC software. Mac and the Mac logo are trademarks of Apple Computer, Inc., registered in the U.S. and other countries. Microsoft, Windows and the Windows logo are either registered trademarks or trademarks of Microsoft Corporation in the United States and other countries.
All the system requirements on this page are requirements for the most recent versions of the products. For requirements for older versions, please refer to the user manual for that specific version.
