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• Introduction
  • The concept of CLC Microbial Genomics Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Microbial template workflows
  • Taxonomic Analysis template workflows
    • Data QC and Remove Background Reads
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
    • QC, Assemble and Bin Pangenomes
  • Amplicon-Based Analysis template workflows
    • Data QC and OTU Clustering
    • Detect Amplicon Sequence Variants and Assign Taxonomies
    • Estimate Alpha and Beta Diversities
  • Typing and Epidemiology template workflows
    • Compare Variants Across Samples
    • Create MLST Scheme with Sequence Types
    • Map to Specified Reference
    • Type Among Multiple Species
    • Type a Known Species
  • QIAseq Analysis template workflows
    • Analyze QIAseq xHYB Mycobacterium Tuberculosis Panel Data (Human host)
    • Analyze QIAseq xHYB Viral Panel Data (Human host)
    • Find QIAseq xHYB AMR Markers (Human host)
  • QIAseq Panel Analysis Assistant
• De Novo Assemble Metagenome
• Amplicon-Based Analysis
  • Normalize OTU Table by Copy Number
  • Filter Samples Based on Number of Reads
  • OTU clustering
    • OTU clustering parameters
    • OTU clustering outputs
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Detect Amplicon Sequence Variants
    • Detect Amplicon Sequence Variants parameters
    • Detect Amplicon Sequence Variants output
    • Importing ASV abundance tables
  • Classify Long Read Amplicons
    • Classify Long Read Amplicons parameters
    • Classify Long Read Amplicons output
• Taxonomic Analysis
  • Contig Binning
    • Bin Pangenomes by Taxonomy
    • The Taxonomy Binning Report
    • Bin Pangenomes by Sequence
  • Taxonomic Profiling
    • Taxonomic Profiling parameters
    • Taxonomic Profiling output
    • Taxonomic Profiling abundance table
  • Identify Viral Integration Sites
    • The Viral Integration Viewer
    • The Viral Integration Report
• Abundance Analysis
  • Merge Abundance Tables
  • Refine Abundance Table
    • Refine Abundance Table parameters
    • Refine Abundance Table output
  • Assign Taxonomies to Sequences in Abundance Table
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
    • Clustering of features and samples
    • The heat map view
    • Create heat map for specific taxonomic level
  • Add Metadata to Abundance Table
• Find the best matching reference
  • Find Best Matches using K-mer Spectra
    • From samples best matches to a common reference for all
  • Find Best References using Read Mapping
    • The Find Best References using Read Mapping Report
• Phylogenetic trees using SNPs or k-mers
  • Create SNP Tree
    • SNP tree report
    • SNP tree
    • SNP Matrix
  • Create K-mer Tree
    • Visualization of K-mer Tree for identification of common reference
• MLST Scheme Tools
  • Getting started with the MLST Scheme tools
  • MLST Scheme Visualization and Management
  • Minimum Spanning Trees
    • The Minimum Spanning Tree view
    • Navigating the Tree view
    • The Layout panel
    • The Metadata panel
  • Type With MLST Scheme
    • Type With MLST Scheme results
    • The MLST Typing Result element
  • Add Typing Results to MLST Scheme
  • Identify MLST Scheme from Genomes
• Additional Typing Tools
  • Spoligotype Mycobacterium Tuberculosis
    • Spoligotype Mycobacterium Tuberculosis parameters
    • Spoligotype Mycobacterium Tuberculosis output
• Functional Analysis
  • Find Prokaryotic Genes
  • Annotate with BLAST
  • Annotate with DIAMOND
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Best DIAMOND Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
    • Functional profile abundance table
  • Infer Functional Profile
  • Identify Pathways
    • Called Pathways Result
    • The Identified Pathways View
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide Database
  • Find Resistance with ShortBRED
    • Resistance abundance table
  • Join Nearby Variants
• Databases for MLST Schemes
  • Create MLST Scheme
  • Download MLST Scheme
  • Import MLST Scheme
• Databases for Amplicon-Based Analysis
  • Download Amplicon-Based Reference Database
• Databases for Taxonomic Analysis
  • Download Curated Microbial Reference Database
    • Extracting a subset of a database
  • Download Custom Microbial Reference Database
    • Database Builder
  • Download Pathogen Reference Database
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download Ontology Database
    • The GO Database View
    • The EC Database View
  • Download Pathway Database
    • The Pathway Database
    • The Pathway View
  • Create DIAMOND Index
  • Import RNAcentral Database
  • Import PICRUSt2 Multiplication Table
• Databases for Drug Resistance Analysis
  • Download Resistance Database
  • Reference Data Elements
• QIAseq 16S/ITS Demultiplexer
• Utility Tools
  • Create Report from Table
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
  • Result Metadata
    • Create a Result Metadata Table
    • Running an analysis directly from a Result Metadata Table
    • Extend Result Metadata Table
    • Use Genome as Result
• Legacy tools
  • Extract Regions from Tracks
  • Analyze Viral Hybrid Capture Panel Data
• Appendix
  • Using the Assembly ID annotation
• Bibliography

Installing modules

Note: In order to install plugins and modules, the CLC Workbench must be run in administrator mode. On Windows, you can do this by right-clicking the program shortcut and choosing "Run as Administrator". On Linux and Mac, it means you must launch the program such that it is run by an administrative user.

Plugins and modules are installed and uninstalled using the Workbench Plugin Manager. To open the Plugin Manager, click on the Plugins () button in the top Toolbar, or go to the menu option:

Utilities | Manage Plugins... ()

The Plugin Manager has two tabs at the top:

• Manage Plugins An overview of your installed plugins and modules is provided under this tab.
• Download Plugins Plugins and modules available to download and install are listed in this tab.

To install a plugin, click on the Download Plugins tab (figure 1.1). Select a plugin. Information about it will be shown in the right hand panel. Click on the Download and Install button to install the plugin.

Figure 1.1: Plugins and modules available for installation are listed in the Plugin Manager under the Download Plugins tab.

Accepting the license agreement

The End User License Agreement (EULA) must be read and accepted as part of the installation process. Please read the EULA text carefully, and if you agree to it, check the box next to the text I accept these terms. If further information is requested from you, please fill this in before clicking on the Finish button.

Installing a cpa file

If you have a .cpa installer file for CLC Microbial Genomics Module, you can install it by clicking on the Install from File button at the bottom of the Plugin Manager.

If you are working on a system not connected to the internet, plugin and module .cpa files can be downloaded from https://digitalinsights.qiagen.com/products-overview/plugins/using a networked machine, and then transferred to the non-networked machine for installation.

Restart to complete the installation

Newly installed plugins and modules will be available for use after restarting the software. When you close the Plugin Manager, a dialog appears offering the opportunity to restart the CLC Workbench.

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Subsections

• Licensing modules
• Uninstalling modules

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