Manuals
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Introduction to the CLC Microbial Genomics Module
The concept of the CLC Microbial Genomics
Contact information
Contact for the CLC Workbench
New program feature request
Getting help
System requirements and installation
System requirements
Installation of modules
Workbench Licenses
Uninstalling modules
Server Licenses
Clustering of Operational Taxonomic Units
Download OTU Reference Database
Format Reference Database
Optional Merge Paired Reads
Fixed Length Trimming
Filter Samples Based on the Number of Reads
OTU clustering
OTU clustering parameters
OTU clustering tool outputs
Visualization of the OTU abundance table
Remove OTUs with Low Abundance
Add Metadata to Abundance Table
Estimation of Alpha and Beta diversity
Align OTUs with MUSCLE
Alpha Diversity
Alpha diversity measures
Beta Diversity
Beta diversity measures
PERMANOVA Analysis
Convert Abundance Table to Experiment
Importing OTU abundance tables
Workflows
Data QC and OTU Clustering workflow
Estimate Alpha and Beta Diversities workflow
Introduction to Typing and Epidemiology (beta)
Workflow templates
Typing samples of a single known species
Preliminary steps to run the 'Type a Known Species' workflow
How to run the 'Type a Known Species' workflow for a single sample
Example of results obtained using the Type a Known Species workflow
How to run the 'Type a Known Species' workflow on a batch of samples:
Typing of samples among multiple species
Preliminary steps to run the 'Type Multiple Species' workflow
How to run the 'Type Among Multiple Species' workflow for a single sample
Example of results obtained using the Type Among Multiple Species workflow
How to run the 'Type Among Multiple Species' workflow on a batch of samples:
Map to a specified common 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:
Handling of metadata and analysis results
Introduction to setting up and managing Metadata Tables
Associating data elements with metadata
Create a Result Metadata Table
Add to Result Metadata Table
Use Genome as Result
Running analysis directly from a Result Metadata Table
Filtering in Result Metadata Table
Example of filtering in a SNP-Tree creation scenario
Working with bacterial genomes databases
Download Bacterial Genomes from NCBI
Download Pathogen Reference Databases
Set Up Pathogen Reference Database
Extracting a subset of NCBI's bacterial genomes database
Find the best matching reference
Find Best Matches using K-mer Spectra
From samples best matches to a common reference for all
Resistance typing
Download Database for Find Resistance
Set Up Resistance Gene Database
Find Resistance
NGS MLST
Download, create, add to and merge MLST schemes
Download MLST Schemes
Download other MLST Schemes
Create MLST Schemes
Merge MLST Schemes
Add Sequences to MLST Schemes
Add NGS MLST Report to Scheme
Schemes visualization and management
Identify MLST Scheme for Genomes
Identify MLST
Extract Regions from Tracks
Phylogenetic trees using SNPs or k-mers
Create SNP Tree
SNP tree output report
Visualization of SNP Tree including metadata and analysis result metadata
SNP Tree Variants editor viewer
Create K-mer Tree
Visualization of K-mer Tree for identification of common reference
Introduction to whole metagenomics analysis (beta)
Functional metagenome analysis tools
Download GO Database
De Novo Assemble Metagenome
Annotate CDS with Best BLAST Hit
Annotate CDS with Pfam Domains
Build Functional Profile
Merge Abundance Tables
Licensing requirements for the CLC Microbial Genomics Module
Workbenches licenses
Request an evaluation license
Download a license using a license order ID
Import a license from a file
Configure license server connection
Download a static license on a non-networked machine
Server licenses
Static license installation
Windows license download
Mac OS license download
Linux license download
Download a static license on a non-networked machine
Network license installation
Bibliography
Functional metagenome analysis tools
Subsections
Download GO Database
De Novo Assemble Metagenome
Annotate CDS with Best BLAST Hit
Annotate CDS with Pfam Domains
Build Functional Profile
Merge Abundance Tables
