Description
CLC Genomics Workbench is a powerful software solution and a complete suite of tools in the fields of genomics, modeling, epigenetics, and meta-genomics that helps scientists and professionals use advanced technology, unique features, and algorithms to step by step solve the challenges of analyzing genetic information. This user-friendly bioinformatics software allows you to thoroughly analyze your NGS data. You can also find relationships between symbiotic microorganisms and explore complex meta-genomic data easily with this software.
CLC Genomics Workbench software supports NGS platforms such as Illumina, ionTorrent, PacBio, and GeneReader and provides cell RNA workflows for various analyses at gene levels. The software also lets you make important discoveries in human disease research and perform your best analysis.
Features of CLC Genomics Workbench Software:
- Genetic data analysis
- Using advanced technologies and algorithms
- NGS data analysis
- Professional and attractive user interface
- Conduct research and analyze information in the biological sciences
System Requirements
V23:
This page lists the requirements for all CLC software products, plugins and special use cases. The requirements for the Biomedical Genomics Analysis Plugin, CLC Single Cell Analysis Module, CLC Microbial Genomics Module are different and are listed separately below, as are special use cases requirements for the 3D Molecule Viewer, Read Mapping and De Novo Assembly. Please note that 16 GB of RAM is required to analyze data generated with the QIAseq Panel using Biomedical Genomics Analysis, 24 GB is recommended.
Qiagen CLC Genomics Workbench
, Standard requirements without using functionality in plugins
- Windows 10, Windows 11, Windows Server 2012, Windows Server 2016, Windows Server 2019, and Windows Server 2022
- Mac: macOS 11, 12, and 13
- Linux: RHEL 7 and later, SUSE Linux Enterprise Server 12 and later. The software is expected to run without problems on other recent Linux systems, but we do not guarantee this. To use BLAST related functionality, libnsl.so.1 is required.
- 64 bit operating system
- 16GB RAM recommended (8GB RAM required)
- 1024 x 768 display required
- 1600 x 1200 display recommended
Memory and CPU settings for reading mappings
Mapping the human genome (3.2 gigabases), or a genome of similar size, requires 16 GB of RAM. Smaller systems can be used when mapping smaller genomes.
Larger amounts of memory can help the overall speed of analysis when working with large datasets, but expect little benefit above about 32 GB of RAM.
Increasing the number of CPUs can reduce the time taken for read mapping, however, the performance gain is expected to be limited above approximately 40 threads.
System requirements for 3D viewers
A graphics card that supports OpenGL 2.0.
Comment: 3D rendering is only supported if CLC Genomics Workbench is installed on the same machine on which the viewer is opened. Indirect rendering (such as X11 forwarding via ssh), remote desktop connections/VNC, and running in virtual machines are not supported.
Plugins and modules
Biomedical Genomics Analysis Plugin
The system requirements for Biomedical Genomics Analysis are similar to those of the CLC Genomics Workbench except for the following:
- 16 GB RAM required
- 24GB RAM recommended
- Minimum 100 GB free disk space in the tmp directory
- A minimum of 90 GB of free disk space is required in the CLC_REFERENCES directory of the CLC Workbench if you are not connecting to a CLC server and not using the CLC_REFERENCES area on that server. The reference data location on the CLC Workbench can be changed from the default location, as described in Reference Data Manager.
Special requirements for QIAseq analysis
The following use cases have specific system requirements
- UPX 3′ or UPXome analysis on multiple samples sometimes requires more than 24 GB of RAM.
- For full exome, multimodal pan cancer or TMB analysis, we recommend running on a server (see requirements below). The number of cores significantly affects the runtime.
CLC Lightspeed Module
The system requirements for the CLC LightSpeed Module are the same as those for the CLC Genomics Workbench, except for the following:
- All LightSpeed analyses require 32 GB of RAM.
- A CPU that supports the AVX2 or NEON instruction set is required.
CLC Single Cell Analysis Module
The system requirements of the CLC Single Cell Analysis module are the same as those of the CLC Genomics Workbench, except for the following:
Most tools can be run on modest hardware such as a laptop, especially when the number of cells is less than 50,000.
Special Requirements for Mapping Reads
For mapping reads to references, we recommend using the CLC Genomics Server (see requirements below). Although a laptop with 16 GB RAM can be used, the large number of reads is likely to result in long run times when there are more than 1000 cells.
Long Read Support (Beta) Plugin
The system requirements for the Long Read Support (Beta) plugin are the same as those for the CLC Genomics Workbench, except for the following:
- The tool requires a CPU that supports the AVX2 or NEON instruction set.
CLC Microbial Genomics Module
The system requirements of the CLC Microbial Genomics Module are the same as those of the CLC Genomics Workbench, except for the following:
- Tools using Diamond and Shortbread require a CPU that supports the AVX2 or NEON instruction sets.
Special Requirements for the MLST Planning Tool
System requirements for MLST planning tools depend on the size of the MLST plans (both the number of alleles and the number of sequence types). A laptop with 16 GB of memory is typically sufficient for 7-gene plans or cgMLST plans based on a moderate number of isolates. Larger plans may require more memory for typing or creating, and in general, we recommend at least 64 GB of memory when working with cg/wgMLST plans based on more than 100 isolates.
Special Requirements for a Taxonomic Profiler
The quality performance of the Taxonomic Profiler depends on the reference database used – the more complete the 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 of RAM. When creating your reference database with the Download Microbial Reference Database tool, you will receive a warning about the memory requirements needed to run the Taxonomic Profiler with this database.
Special requirements for de novo assembled metagenomes
It is recommended to have at least 16 GB of RAM when running a de novo assembled metagenome.
other requirements
PCOA 3D Viewer The requirements are similar to the 3D Viewer requirements described in the CLC Genomics Workbench section above.
Sunrise Viewer Uses 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.
V22:
- Windows 7, Windows 8, Windows 10, Windows 11, Windows Server 2012, Windows Server 2016, and Windows Server 2019
- Mac: macOS 10.15, macOS 11 through macOS 12.01. Macs with the Apple M1 chip are supported. The software is expected to run without issues on more recent macOS releases than those listed, but we do not guarantee this.
- Linux: RHEL 7 and later, SUSE Linux Enterprise Server 12 and later. The software is expected to run without problems on other recent Linux systems, but we do not guarantee this. To use BLAST related functionality, libnsl.so.1 is required.
- 64 bit operating system
- 2 GB RAM required
- 4GB RAM recommended
- 1024 x 768 display required
- 1600 x 1200 display recommended
- Requires Intel or AMD CPU
Special requirements for the 3D molecule viewer
- Required: A graphics card capable of supporting OpenGL 2.0.
- Required: Updated graphics driver. Please make sure the latest driver for the graphics card is installed.
- Recommended: A discrete graphics card from Nvidia or AMD/ATI. Modern integrated graphics cards (such as the Intel HD Graphics series) can also be used, but these are usually slower than discrete cards.
- Note: indirect rendering (such as x11 forwarding via ssh), Remote Desktop Connection/VNC, and running in virtual machines are not supported.
Special requirements for read mapping
The numbers below give the minimum and recommended memory for a system running mapping and analysis tasks. The suggested requirements are based on genome size.
- E. coli K12 (4.6 megabases)
- Minimum: 2GB RAM
- Recommended: 4GB RAM
- C. elegans (100 megabases) And Arabidopsis thaliana (120 megabases)
- Minimum: 2GB RAM
- Recommended: 4GB RAM
- Zebrafish (1.5 Gigabases)
- Minimum: 2 GB RAM
- Recommended: 4GB RAM
- Human (3.2 Gigabase) And Mouse (2.7 Gigabytes)
- Minimum: 6 GB RAM
- Recommended: 8GB RAM
Special requirements for de novo assembly
De novo Assembly may require more memory than indicated above – this depends on both the number of reads, the error profile, and the complexity and size of the genome.
Pictures
version: New in the v22 and 21 releases, QIAGEN CLC Genomics now has three major offerings, ranging from basic to packages (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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