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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
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
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
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
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
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 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
- 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
  - ARES Database
- Set Up Gene Database
QIAseq 16S/ITS Demultiplexer
Appendices
- Using the Assembly ID annotation
- Legacy tools
- Licensing requirements for the CLC Microbial Genomics Module
  - Workbench licenses
  - Server licenses
Bibliography

Preliminary steps to run the Type Multiple Species workflow

Before starting the workflow,

Download microbial genomes using either the Download or Set Up Microbial Reference Database tools or the Download Pathogen Reference Database tool (see the Working with databases chapter).
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).

Your Navigation Area should now look similar to the figure 25.17.

Image databases_schemes2
Figure 25.17: Overview of the Navigation area after downloading the databases and schemes necessary to run the workflows.