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Introduction to CLC Microbial Genomics Module
- 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 OTU clustering
- Filter Samples Based on the Number of Reads
- OTU clustering
- Remove OTUs with Low Abundance
- Align OTUs with MUSCLE
- Amplicon-Based OTU Clustering Workflows
  - Data QC and OTU Clustering workflow
  - Estimate Alpha and Beta Diversities workflow
Taxonomic Analysis
- Taxonomic Profiling
  - Taxonomic profiling abundance table
  - Taxonomic Profiling report
- Workflows
Functional analysis
- Annotate CDS with Best BLAST Hit
- Annotate CDS with Pfam Domains
- Build Functional Profile
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
Resistance typing
- Find Resistance
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 Taxonomic Profiling
- Create Microbial Reference Database
- Set Up Microbial Reference Database
- Download Pathogen Reference Database
  - Extracting a subset of a database
  - Download Pathogen Reference Database output report
Databases for Functional Analysis
- Download Database for Find Resistance
- Set Up Gene Database
- Download GO Database
Databases for Amplicon-Based Analysis
- Download Amplicon-Based Reference Database
- Set Up Amplicon-Based Reference Database
Databases for NGS-MLST
- NGS MLST Databases
Legacy tools
- Optional Merge Paired Reads
- Fixed Length Trimming
Licensing requirements for the CLC Microbial Genomics Module
- Workbench licenses
- Server licenses
Bibliography

Download Database for Find Resistance

The Download Database for Find Resistance tool automatically downloads the database from https://cge.cbs.dtu.dk/services/data.php. To run the tool, go to:

Microbial Genomics Module () | Databases () | Functional Analysis | Download Database for Find Resistance ()

Specify a location to save the database. We recommend to use a folder where you save all the databases and MLST schemes necessary to run the CLC Microbial Genomics Module tools. Click Finish.

The output is a sequence list that can be visualized as a table as well. In the table view, users can review the metadata associated with the sequences. It is possible to edit all metadata values, or to delete a gene in a resistance gene database such that users can keep their database up-to-date within the workbench.

It is also possible to merge two resistance gene databases, for example to merge a custom database with the one obtained using the Download Database for Find Resistance tool, or to add new genes to an existing database.