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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
  - Data QC and OTU Clustering workflow
  - Estimate Alpha and Beta Diversities workflow
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
- 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
- Add to Result Metadata Table (legacy)
- Use Genome as Result
Workflow templates
- Map to Specified Reference
  - How to run the Map to Specified Reference workflow
- Type Among Multiple Species
- Type a Known Species
- Extract Regions from Tracks
- Create Large MLST Scheme with Sequence Types
- Compare Variants Across Samples
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
Large MLST Scheme Tools
- Getting started with the Large MLST Scheme tools
- Large MLST Scheme Visualization and Management
- Minimum Spanning Trees
- Type With Large MLST Scheme
  - Type With Large MLST Scheme results
  - The Large MLST Typing Result element
- Add Typing Results to Large MLST Scheme
- Identify Large 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
Drug Resistance Analysis
- Find Resistance with PointFinder
- Find Resistance with Nucleotide DB
- Find Resistance with ShortBRED
  - Resistance abundance table
Databases for Large MLST Schemes
- Create Large MLST Scheme
- Download Large MLST Scheme
- Import Large 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
  - Download Pathogen Reference Database output report
- Create Taxonomic Profiling Index
Databases for Functional Analysis
- Download Protein Database
- Download Ontology Database
  - The GO Database View
  - The EC Database 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
- Split Sequence List
- Create Annotated Sequence List
  - Examples of databases
- Mask Low-Complexity Regions
  - Mask Low-Complexity Regions Report
Appendices
- Using the Assembly ID annotation
- Legacy tools
- 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

Licensing requirements for the CLC Microbial Genomics Module

To use tools delivered by the CLC Microbial Genomics Module or CLC Microbial Genomics Server Extension, you will need a license. This chapter describes how to install and configure such licenses on a CLC Workbench or CLC Server. CLC Microbial Genomics Module can be installed in Viewing Mode on a CLC Workbench to access data created using the module's tools without requiring a license.

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