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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 the 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
Functional analysis
- Find Prokaryotic Genes (beta)
- 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 ResFinder
- Find Resistance with ShortBRED
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
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

Visualization of SNP Tree including metadata and analysis result metadata

The overall tree layout, node- and label settings (figure 14.11) is defined by selected Tree Settings (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Tree_Settings.html).

The creation of a SNP tree allows for the associated Result Metadata Table to be specified. Thus it is possible to visualize the associated metadata as well as analysis result metadata on the phylogenetic tree. This makes it easier to find potential correlations across samples and verify, such as how well MLST typing and the tree topology fit together.

Image snp_tree_meta
Figure 14.11: Visualization of SNP tree including selected metadata and analysis result metadata.