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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 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
    • SNP Matrix
  • 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
  • Workbench 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
    • macOS license download
    • Linux license download
    • Download a static license on a non-networked machine
    • Network license installation
• Bibliography

Working with databases

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Subsections

• Create Microbial Reference Database
• Download Pathogen Reference Database
• 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

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