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Introduction
- The concept of CLC Microbial Genomics Module
- Contact information
System requirements and installation
- System requirements
- Installation of modules
- Plugins licenses
- Uninstalling modules
- Server License
Introduction to Metagenomics
De Novo Assemble Metagenome
Amplicon-Based Analysis
- 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
- 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 (beta)
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
- Add to Result Metadata Table
- Use Genome as Result
Workflow templates
- Map to Specified Reference
  - How to run the Map to Specified Reference workflow on a single sample
  - How to run the Map to Specified Reference workflow on a batch of samples
- Type Among Multiple Species
- Type a Known Species
- Extract Regions from Tracks
Find the best matching reference
- Find Best Matches using K-mer Spectra
- From samples best matches to a common reference for all
Phylogenetic trees using SNPs or k-mers
- Create SNP Tree
- Create K-mer Tree
  - Visualization of K-mer Tree for identification of common reference
NGS MLST
- Schemes visualization and management
- Identify MLST
- Identify MLST Scheme from Genomes
Functional Analysis
- Find Prokaryotic Genes
- Annotate CDS with Best BLAST Hit
- Annotate CDS with Best DIAMOND Hit
- Annotate CDS with Pfam Domains
- Build Functional Profile
  - Functional profile abundance table
Drug Resistance Analysis
- Find Resistance with PointFinder
- Find Resistance with Nucleotide DB
- Find Resistance with ShortBRED
  - Resistance abundance table
Databases for NGS-MLST
- Download MLST Schemes
- Download other MLST Schemes
- Create MLST Schemes
- Add NGS MLST Report to Scheme
- Merge MLST Schemes
- Add Sequences to MLST Schemes
Databases for Amplicon-Based Analysis
- Download Amplicon-Based Reference Database
- Set Up Amplicon-Based Reference Database
Databases for Taxonomic Analysis
- Download Microbial Reference Database
- Set Up Microbial Reference Database
- Download Pathogen Reference Database
  - Extracting a subset of a database
  - Download Pathogen Reference Database output report
- Create Taxonomic Profiling Index
Databases for Functional Analysis
- Download Protein Database
- Download GO Database
- Create DIAMOND Index
Databases for Drug Resistance Analysis
- Download Resistance Database
- Set Up Gene Database
QIAseq 16S/ITS Demultiplexer
Legacy tools
- Optional Merge Paired Reads
- Fixed Length Trimming
Licensing requirements for the CLC Microbial Genomics Module
- Workbench licenses
- Server licenses
Bibliography

Handling of metadata and analysis results

When typing and/or performing epidemiological studies of microbes, sample information such as taxonomy, date of isolation, original source of the sample, etc, may be relevant for data interpretation. Once a CLC Genomics Workbench version 12.0 is installed on your computer, CLC Microbial Genomics Module facilitates the organization and management of such additional data elements (metadata) in a tabular form. In addition, CLC Microbial Genomics Module facilitates the organization and management of generated analysis results and enables these to be shown as decorations on phylogenetic trees.

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