Manuals
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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
Workbench Licenses
Uninstalling modules
Server Licenses
Introduction to Metagenomics
Amplicon-based OTU clustering
Filter Samples Based on the Number of Reads
OTU clustering
OTU clustering parameters
OTU clustering tool outputs
Visualization of OTU abundance tables
Importing and exporting OTU abundance tables
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
Data QC and Clean Host DNA
Data QC and Taxonomic Profiling
Merge and Estimate Alpha and Beta diversities
Functional analysis
De Novo Assemble Metagenome
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
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:
Type a 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:
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
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
NGS MLST
Schemes visualization and management
Identify MLST
Identify MLST Scheme from Genomes
Working with databases
Create Microbial Reference Database
Download Pathogen Reference Database
Extracting a subset of a database
Download Pathogen Reference Database output report
Set Up Microbial Reference Database
Download Database for Find Resistance
Set Up Gene Database
Download Amplicon-Based Reference Database
Set Up Amplicon-Based Reference Database
Download GO Database
NGS MLST Databases
Download MLST Schemes
Download other MLST Schemes
Create MLST Schemes
Add NGS MLST Report to Scheme
Merge MLST Schemes
Add Sequences to MLST Schemes
Legacy tools
Optional Merge Paired Reads
Fixed Length Trimming
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 computer
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
Licensing requirements for the CLC Microbial Genomics Module
Subsections
Workbenches licenses
Server licenses
