Manuals

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Introduction to the CLC Microbial Genomics Module
- The concept of the CLC Microbial Genomics
- Contact information
System requirements and installation
Clustering of Operational Taxonomic Units
Estimation of Alpha and Beta diversity
Workflows
- Data QC and OTU Clustering workflow
- Estimate Alpha and Beta Diversities workflow
Introduction to Typing and Epidemiology (beta)
Workflow templates
Handling of metadata and analysis results
Working with bacterial genomes databases
Find the best matching reference
- Find Best Matches using K-mer Spectra
- From samples best matches to a common reference for all
Resistance typing
NGS MLST
Phylogenetic trees using SNPs or k-mers
- Create SNP Tree
- Create K-mer Tree
  - Visualization of K-mer Tree for identification of common reference
Introduction to whole metagenomics analysis (beta)
Functional metagenome analysis tools
Licensing requirements for the CLC Microbial Genomics Module
- Workbenches licenses
- Server licenses
Bibliography

Working with bacterial genomes databases

Subsections

Download Bacterial Genomes from NCBI
Download Pathogen Reference Databases
Set Up Pathogen Reference Database
Extracting a subset of NCBI's bacterial genomes database