Published on: 2023-06-08 15:26:46
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The CLC Genomics Workbench is a powerful software solution and a complete suite of tools in the field of genomics , modeling, epigenetics, and meta-genomics that help scientists and professionals utilize advanced technology, unique features, and algorithms. Slowly address the challenges of analyzing genetic information. This user-friendly bioinformatics software allows you to fully analyze your NGS data. You can also find relationships between symbiotic microorganisms with this software and easily explore complex meta-genomic data.
The CLC Genomics Workbench software supports NGS platforms such as Illumina, IonTorrent, PacBio and GeneReader and provides cell RNA workflows for various analyzes on gene levels. The software also lets you make important discoveries in human disease research and perform your best analysis.
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.
QIAGEN CLC Genomics Workbench
* 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.
Plugins and Modules
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 (beta) plugin
The system requirements of the Long Read Support (beta) plugin are the same as those for the CLC Genomics Workbench, apart from the following:
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
he 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.
Other requirements
The PCoA 3D viewer requirements are the same as the 3D viewer requirements described in the CLC Genomics Workbench section above.
The Sunburst viewer makes use of JavaFX and may not work on older Linux kernels. An updated list of requirements for JavaFX can be found at http://www.oracle.com/technetwork/java/javafx/downloads/supportedconfigurations-1506746.html.
Special requirements for the 3D Molecule Viewer
Special requirements for read mapping
The numbers below give minimum and recommended memory for systems running mapping and analysis tasks. The requirements suggested are based on the genome size.
Special 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.
Editions: New in the v22 and 21 release, QIAGEN CLC Genomics now has three key offerings, with packages ranging from basic (QIAGEN CLC Main Workbench), advanced (QIAGEN CLC Genomics Workbench) and premium (QIAGEN CLC Genomics Workbench Premium), to meet your specific sequence and ‘omics data analysis needs.
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