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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

Preliminary steps to run the Type a Known Species (legacy) workflow

Before starting the workflow,

Download microbial genomes using either the Download Custom Microbial Reference Database or the Download Pathogen Reference Database tool (see the Working with databases chapter). Databases can also be created using the Create Annotated Sequence List.
Download the MLST schemes using the Download MLST Schemes tool (see the Downloading schemes section).
Download the database for the Find Resistance with Nucleotide DB tool using the Download Resistance Database tool (see the Download Resistance Database section).
Create a New Result Metadata table using the Create Result Metadata Table tool (see the Create Result Metadata Table section).

When you are ready to start the workflows, your navigation area should look similar to the figure 24.45.

Image legacy_databases_schemes
Figure 24.45: Overview of the Navigation area after creating the result metadata table and downloading the databases and MLST schemes necessary to run the workflows.