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Introduction
- The concept of QIAGEN 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 Small Genome
- De Novo Assemble Small Genome parameters
- De Novo Assemble Small Genomes output
De Novo Assemble Metagenome
- De Novo Assemble Metagenome parameters
- De Novo Assemble Metagenome output
Amplicon-Based Analysis
- Normalize OTU Table by Copy Number
- Filter Samples Based on Number of Reads
- OTU clustering
- Align OTUs using MUSCLE
- Detect Amplicon Sequence Variants
- Classify Long Read Amplicons
  - Classify Long Read Amplicons parameters
  - Classify Long Read Amplicons output
Taxonomic Analysis
- Contig Binning
- Identify Viral Integration Sites
  - The Viral Integration Viewer
  - The Viral Integration Report
- Classify Whole Metagenome Data
- Taxonomic Profiling
Abundance Analysis
- Merge Abundance Tables
  - Merge Abundance Tables output
- 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
- Type with Consensus Refinement
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
  - Download MLST Scheme parameters
- Import MLST Scheme
Databases for Amplicon-Based Analysis
- Download Amplicon-Based Reference Database
Databases for Taxonomic Analysis
- Download Curated Microbial Reference Database
- Download Custom Microbial Reference Database
  - Database Builder
- Download Pathogen Reference Database
- Create Whole Metagenome Index
- 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
- Mask Low-Complexity Regions
  - Mask Low-Complexity Regions Report
- Result Metadata
Legacy tools
- Remove OTUs with Low Abundance
Appendix
- Using the Assembly ID annotation
Bibliography

Type with Consensus Refinement

The Type with Consensus Refinement tool is inspired by the Iterative Refinement Meta-Assembler (IRMA) tool [Shepard et al., 2016] developed by the Center for Disease Control and Prevention (CDC) in the USA. The primary use for this tool is to assist in the typing of small, segmented viral genomes such as Influenza viruses. The tool works by iteratively mapping the reads to a set of annotated reference sequences, evaluating the quality of the mappings, and extracting consensus sequences. This process is repeated using the consensus sequences as new references until the mapping metrics stabilize, indicating that further iterations will not improve the results.

After finishing the iterative refinement process, the tool transfers all annotations from the references to the consensus sequences. The CDS annotations are translated into protein sequences. These sequences are then checked for unexpected codons at the start and stop positions as well as unexpected internal stop codons that may indicate frameshifts in the consensus.

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