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• Introduction
  • The concept of CLC Microbial Genomics Module
  • Contact information
• System requirements and installation
  • System requirements
  • Installation of modules
  • Licensing modules
  • Uninstalling modules
  • Server License
• Introduction to Metagenomics
• De Novo Assemble Metagenome
• Amplicon-Based Analysis
  • Normalize OTU Table by Copy Number
  • Filter Samples Based on Number of Reads
  • OTU clustering
    • OTU clustering parameters
    • OTU clustering tool outputs
    • Visualization of OTU abundance tables
    • Create taxonomic level subtables for heat maps
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Amplicon-Based Analysis Workflows
• Taxonomic Analysis
  • Contig Binning
    • Bin Pangenomes by Taxonomy
    • Bin Pangenomes by Sequence
  • Taxonomic Profiling
    • Taxonomic profiling abundance table
    • Taxonomic Profiling report
    • Sorted Reads Files
  • Identify Viral Integration Sites
    • The Viral Integration Viewer
    • The Viral Integration Report
  • Taxonomic Analysis Workflows
• 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
  • Extend Result Metadata Table
  • Use Genome as Result
• Find the best matching reference
  • Find Best Matches using K-mer Spectra
  • From samples best matches to a common reference for all
  • Find Best References using Read Mapping
    • The Find Best References using Read Mapping Report
• 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
  • Extract Regions from Tracks
• MLST Scheme Tools
  • Getting started with the MLST Scheme tools
  • 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 MLST Scheme
    • Type With MLST Scheme results
    • The MLST Typing Result element
  • Add Typing Results to MLST Scheme
  • Identify MLST Scheme from Genomes
• Workflow templates
  • Taxonomic Analysis
    • Analyze Viral Hybrid Capture Panel Data
    • Data QC and Remove Background Reads
    • Data QC and Taxonomic Profiling
    • Merge and Estimate Alpha and Beta diversities
    • QC, Assemble and Bin Pangenomes
  • Amplicon-Based Analysis Workflows
    • Data QC and OTU Clustering workflow
    • Estimate Alpha and Beta Diversities workflow
  • Typing and Epidemiology
    • Compare Variants Across Samples
    • Create MLST Scheme with Sequence Types
    • Map to Specified Reference
    • Type Among Multiple Species
    • Type a Known Species
• Functional Analysis
  • Find Prokaryotic Genes
  • Annotate with BLAST
  • Annotate with DIAMOND
  • Annotate CDS with Best BLAST Hit
  • Annotate CDS with Best DIAMOND Hit
  • Annotate CDS with Pfam Domains
  • Build Functional Profile
    • Functional profile abundance table
  • Infer Functional Profile
  • Identify Pathways
    • Called Pathways Result
    • The Identified Pathways View
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide DB
  • Find Resistance with ShortBRED
    • Resistance abundance table
• Databases for MLST Schemes
  • Create MLST Scheme
  • Download MLST Scheme
  • Import MLST Scheme
• Databases for Amplicon-Based Analysis
  • Download Amplicon-Based Reference Database
• Databases for Taxonomic Analysis
  • Download Curated Microbial Reference Database
    • Extracting a subset of a database
  • Download Custom Microbial Reference Database
    • Database Builder
  • Download Pathogen Reference Database
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download Ontology Database
    • The GO Database View
    • The EC Database View
  • Download Pathway Database
    • The Pathway Database
    • The Pathway View
  • Create DIAMOND Index
  • Import RNAcentral Database
  • Import PICRUSt2 Multiplication Table
• Databases for Drug Resistance Analysis
  • Download Resistance Database
    • ARES Database
• QIAseq 16S/ITS Demultiplexer
• Tools
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
• Appendices
  • Using the Assembly ID annotation
  • Legacy tools
    • Legacy MLST schemes visualization and management
  • Licensing requirements for the CLC Microbial Genomics Module
    • Licensing modules on a Workbench
      • 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
    • Licensing Server Extensions on a CLC Server
      • Download a static license on a non-networked machine
• Bibliography

System requirements

To work with CLC Microbial Genomics Module 22.1 you will need to have CLC Genomics Workbench version 22 installed on your computer. With exception of the requirements below, the system requirements of CLC Microbial Genomics Module 22.1 are the same as the ones required for the CLC Genomics Workbench (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=System_requirements.html)

• 8 GB RAM recommended
• Tools using DIAMOND and ShortBRED require CPU with an AVX instruction set

Special requirements for the MLST Scheme tools.

The system requirements for the MLST Scheme tools depend on the size of the MLST schemes (both the number of alleles and the number of sequence types). A laptop with 16GB of memory is normally sufficient for 7-gene schemes or cgMLST schemes based on a moderate number of isolates. Typing or constructing larger schemes may require more memory, and in general, we recommend at least 64GB of memory when working with cg/wgMLST schemes based on more than 100 isolates.

Special requirements for the Taxonomic Profiler.

The quality performance of the Taxonomic Profiler depends on the reference database used - the more complete a database, the better the quality. However, running the Taxonomic Profiler with a given database size will require at least the same amount of memory. For example, running with a 14 GB database requires at least 16 GB of RAM, and running with a 56 GB database requires a minimum of 64 GB RAM. When creating your reference database with the Download Custom Microbial Reference Database tool, you will get a warning about the memory requirements needed for running the Taxonomic Profiler with this database.

Special requirements for De Novo Assemble Metagenome.

It is recommended to have at least 16 GB RAM when running the De Novo Assemble Metagenome.

The PCoA 3D viewer requirements are the same as the 3D Molecule Viewer.

The Sunburst viewer makes use of JavaFX and may not work on older Linux kernels. An updated list of requirements for JavaFX can be found at http://www.oracle.com/technetwork/java/javafx/downloads/supportedconfigurations-1506746.html.

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