• Manuals

Browse the manual

• Introduction
  • 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 Analysis
  • Filter Samples Based on 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 Analysis Workflows
    • Data QC and OTU Clustering workflow
    • Estimate Alpha and Beta Diversities workflow
• Taxonomic Analysis
  • Contig Binning
    • Bin Pangenomes by Taxonomy
    • Bin Pangenomes by Sequence
  • Taxonomic Profiling
    • Taxonomic profiling abundance table
    • Taxonomic Profiling report
    • Sorted Reads Files
  • Workflows
    • Data QC and Clean Host DNA
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
    • QC, Assemble and Bin Pangenomes
• 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
• 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
• 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
• Large MLST Scheme Tools
  • Getting started with the Large MLST Scheme tools
  • Large MLST Scheme Visualization and Management
  • Minimum Spanning Trees
    • The Minimum Spanning Tree view
    • Navigating the Tree view
    • The Layout panel
    • The Metadata panel
  • Type With Large MLST Scheme (beta)
    • Type With Large MLST Scheme results
    • The Large MLST Typing Result element
  • Add Typing Results to Large MLST Scheme (beta)
• Functional Analysis
  • Find Prokaryotic Genes
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Best DIAMOND Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
    • Functional profile abundance table
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide DB
  • Find Resistance with ShortBRED
    • Resistance abundance table
• Databases for NGS-MLST
  • Download MLST Schemes
  • Download other MLST Schemes
  • Create MLST Schemes
  • Add NGS MLST Report to Scheme
  • Merge MLST Schemes
  • Add Sequences to MLST Schemes
• Databases for Large MLST Schemes
  • Create Large MLST Scheme (beta)
  • Download Large MLST Scheme
  • Import Large MLST Scheme
• Databases for Amplicon-Based Analysis
  • Download Amplicon-Based Reference Database
  • Set Up Amplicon-Based Reference Database
• Databases for Taxonomic Analysis
  • Download Microbial Reference Database
  • Set Up Microbial Reference Database
  • Download Pathogen Reference Database
    • Extracting a subset of a database
    • Download Pathogen Reference Database output report
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download GO Database
  • Create DIAMOND Index
• Databases for Drug Resistance Analysis
  • Download Resistance Database
    • ARES Database
  • Set Up Gene Database
• QIAseq 16S/ITS Demultiplexer
• Appendices
  • Using the Assembly ID annotation
  • 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

Databases for Taxonomic Analysis

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Subsections

• Download Microbial Reference Database
• Set Up Microbial Reference Database
• Download Pathogen Reference Database
• Create Taxonomic Profiling Index

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