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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
Introduction to Metagenomics
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
- Amplicon-Based Analysis Workflows
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
- Taxonomic Analysis Workflows
Abundance Analysis
- Merge Abundance Tables
- 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
- Convert Abundance Table to Experiment
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
- Extract Regions from Tracks
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
Workflow templates
- Taxonomic Analysis
- Amplicon-Based Analysis Workflows
  - Data QC and OTU Clustering workflow
  - Estimate Alpha and Beta Diversities workflow
- Typing and Epidemiology
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
- Mask Low-Complexity Regions
  - Mask Low-Complexity Regions Report
Appendices
- Using the Assembly ID annotation
- Legacy tools
  - Legacy MLST schemes visualization and management
- 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
Bibliography

Download Pathway Database

Calling pathways using the Identify Pathways tool requires a pathway database. Such databases can be obtained using the Download Pathway Database tool. To run the Download Pathway Database tool go to

Toolbox | Microbial Genomics Module () | Functional Analysis () | Download Pathway Database ()

In the first step of the wizard a pathway database can be selected. Currently, the only available option is MetaCyc. Upon clicking "Next" the EULA for the selected database will appear, which needs to be accepted before proceeding to the download.

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