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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

Resistance typing

Identification of antimicrobial resistance genes is important for understanding the underlying mechanisms and the epidemiology of antimicrobial resistance. The Find Resistance tool may be used for resistance typing of pre-assembled, complete or partial genomes simple contig sequences assembled using the de novo assembly algorithm of CLC Genomics Workbench (see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=De_novo_assembly.html). Alternatively, use the Type a Known Species or Type among Multiple Species template workflows as described in the chapter Workflow templates.

The Find Resistance tool is inspired by [Zankari et al., 2012] and uses BLAST for identification of acquired antimicrobial resistance genes within whole-genome sequencing (WGS) data.

Subsections

Find Resistance