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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
• Microbial template workflows
  • Taxonomic Analysis template workflows
    • 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 template workflows
    • Data QC and OTU Clustering
    • Detect Amplicon Sequence Variants and Assign Taxonomies
    • Estimate Alpha and Beta Diversities
  • Typing and Epidemiology template workflows
    • Compare Variants Across Samples
    • Create MLST Scheme with Sequence Types
    • Map to Specified Reference
    • Type Among Multiple Species
    • Type a Known Species
  • QIAseq Analysis template workflows
    • Analyze QIAseq xHYB Viral Panel Data
    • Find QIAseq xHYB AMR Markers
• 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 outputs
    • The OTU abundance table
    • Importing and exporting OTU abundance tables
  • Remove OTUs with Low Abundance
  • Align OTUs with MUSCLE
  • Detect Amplicon Sequence Variants
    • Detect Amplicon Sequence Variants parameters
    • Detect Amplicon Sequence Variants output
    • Importing ASV abundance tables
• 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
• Abundance Analysis
  • Merge Abundance Tables
  • Assign Taxonomies to Sequences in Abundance Table
  • Alpha Diversity
    • Alpha diversity measures
  • Beta Diversity
    • Beta diversity measures
  • PERMANOVA Analysis
  • Differential Abundance Analysis
  • Create Heat Map for Abundance Table
    • Clustering of features and samples
    • The heat map view
    • Create heat map for specific taxonomic level
  • Add Metadata to Abundance Table
• 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
• 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
• 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
  • Extract Regions from Tracks
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
• Legacy tools
  • Convert Abundance Table to Experiment
• 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
• Appendices
  • Using the Assembly ID annotation
• Bibliography

System requirements

CLC Microbial Genomics Module 23.0 is for use with CLC Genomics Workbench version 23 or newer. The system requirements for CLC Genomics Workbench are provided at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=System_requirements.html.

The system requirements for CLC Microbial Genomics Module are the same as those for CLC Genomics Workbench, except for the following:

• Tools using DIAMOND and ShortBRED require a CPU that supports the AVX2 or NEON instruction sets.

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. Downloading and constructing or typing with 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 Taxonomic Profiling.

The performance of the Taxonomic Profiling tool depends on the reference database used - the more complete a database, the better the taxonomic profiling. However, running Taxonomic Profiling with a given database size will require at least the same amount of memory. For example, a 14 GB database requires at least 16 GB of RAM, and 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 Profiling tool 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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