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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
- Amplicon-Based Analysis template workflows
- Typing and Epidemiology template workflows
- QIAseq Analysis template workflows
- 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
- Remove OTUs with Low Abundance
- Align OTUs with MUSCLE
- Detect Amplicon Sequence Variants
- Classify Long Read Amplicons
  - Classify Long Read Amplicons parameters
  - Classify Long Read Amplicons output
Taxonomic Analysis
- Contig Binning
- Taxonomic Profiling
- 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
- 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
- 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
- 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
Legacy tools
- Extract Regions from Tracks
- Analyze Viral Hybrid Capture Panel Data
Appendix
- Using the Assembly ID annotation
Bibliography

Legacy tools

The documentation in this section is for tools that have been deprecated and that will be retired in a future version. In most cases, deprecated tools can be found in the Legacy Tools (

) folder of the Workbench Toolbox, with "(legacy)" appended to their names to highlight their status.

We recommend redesigning workflows containing any of these tools to remove them. Where a new tool has been introduced to take the deprecated tool's place, please try including the new tool.

If you have concerns about the retirement of particular tools in this section, please contact QIAGEN Bioinformatics Support team at ts-bioinformatics@qiagen.com.

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