• 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
  • Importing OTU abundance tables
• Alpha and Beta Diversity
  • Align OTUs with MUSCLE
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
• Statistical analyses
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
  • Legacy Convert Abundance Table to Experiment
• 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
  • 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
    • Example of filtering in a SNP-Tree creation scenario
  • Add to Result Metadata Table
  • Use Genome as Result
• 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

Statistical analyses

The tools described in this chapter can be used using OTU abundance tables or functional abundance tables as input.

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Subsections

• Differential Abundance Analysis
• Create Heat Map for Abundance Table
• Legacy Convert Abundance Table to Experiment

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