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Introduction
- The concept of CLC Microbial Genomics Module
- Contact information
System requirements and installation
- System requirements
- Installation of modules
- Licensing modules
- Uninstalling modules
- Server License
Microbial template workflows
- Taxonomic Analysis template workflows
- Amplicon-Based Analysis template workflows
- Typing and Epidemiology template workflows
- QIAseq Analysis template workflows
  - Analyze QIAseq xHYB Viral Panel Data
  - Find QIAseq xHYB AMR Markers
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
Taxonomic Analysis
- Contig Binning
  - Bin Pangenomes by Taxonomy
  - Bin Pangenomes by Sequence
- Taxonomic Profiling
- Identify Viral Integration Sites
  - The Viral Integration Viewer
  - The Viral Integration Report
Abundance Analysis
- Merge Abundance Tables
- 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
Introduction to Typing and Epidemiology
Handling of metadata and analysis results
- Importing Metadata Tables
- Associating data elements with metadata
- Create a Result Metadata Table
- Running an analysis directly from a Result Metadata Table
  - Filtering in Result Metadata Table
  - Filtering in a SNP-Tree creation scenario
- Extend Result Metadata Table
- Use Genome as Result
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
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 DB
- Find Resistance with ShortBRED
  - Resistance abundance table
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
  - ARES Database
QIAseq 16S/ITS Demultiplexer
Tools
- Extract Regions from Tracks
- Mask Low-Complexity Regions
  - Mask Low-Complexity Regions Report
Legacy tools
- Convert Abundance Table to Experiment
Licensing requirements for the CLC Microbial Genomics Module
- Licensing modules on a Workbench
- Licensing Server Extensions on a CLC Server
  - Download a static license on a non-networked machine
Appendices
- Using the Assembly ID annotation
Bibliography

MLST Scheme Tools

The typing and characterization of pathogenic isolates plays an important part in epidemiology and outbreak analysis. MLST (Multilocus Sequence Typing) makes it possible to efficiently type strains against schemes with known isolates.

Whereas classic MLST analysis types isolates against a small set of gene fragments (typical 500bp fragments for a set of seven house-keeping genes), cgMLST (core-genome MLST) and wgMLST (whole-genome MLST) extends the analysis to thousands of loci, usually containing the complete coding gene sequences for the alleles for a given locus.

This section of the manual describes the MLST Scheme tools, which can be used to work with both cgMLST and wgMLST, as well as classic 7-gene schemes. The MLST Scheme typing can be applied either directly to the NGS reads of an isolate, or to an assembly of an isolate.

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