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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
    • 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
  • Identify Viral Integration Sites
    • The Viral Integration Viewer
    • The Viral Integration Report
  • Workflows
    • Analyze Viral Hybrid Capture Panel Data
    • 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
  • Extend Result Metadata Table
  • Add to Result Metadata Table (legacy)
  • Use Genome as Result
• Workflow templates
  • Map to Specified Reference
    • How to run the Map to Specified Reference workflow
  • Type Among Multiple Species
    • Preliminary steps to run the Type Among Multiple Species workflow
    • How to run the Type Among Multiple Species workflow
    • Example of results obtained using the Type Among Multiple Species workflow
  • Type a Known Species
    • Preliminary steps to run the Type a Known Species workflow
    • How to run the Type a Known Species workflow
    • Example of results obtained using the Type a Known Species workflow
  • Extract Regions from Tracks
  • Create Large MLST Scheme with Sequence Types
  • Compare Variants Across Samples
• 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
• 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
    • Type With Large MLST Scheme results
    • The Large MLST Typing Result element
  • Add Typing Results to Large MLST Scheme
  • Identify Large 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
• Drug Resistance Analysis
  • Find Resistance with PointFinder
  • Find Resistance with Nucleotide DB
  • Find Resistance with ShortBRED
    • Resistance abundance table
• Databases for Large MLST Schemes
  • Create Large MLST Scheme
  • Download Large MLST Scheme
  • Import Large 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
    • Download Pathogen Reference Database output report
  • Create Taxonomic Profiling Index
• Databases for Functional Analysis
  • Download Protein Database
  • Download Ontology Database
    • The GO Database View
    • The EC Database 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
  • Split Sequence List
  • Create Annotated Sequence List
    • Examples of databases
  • Mask Low-Complexity Regions
    • Mask Low-Complexity Regions Report
• Appendices
  • Using the Assembly ID annotation
  • Legacy tools
    • Optional Merge Paired Reads
    • Fixed Length Trimming
    • MLST tools (legacy)
    • Schemes visualization and management
    • Identify MLST
    • Identify MLST Scheme from Genomes
    • Download MLST Schemes
    • Download other MLST Schemes
    • Create MLST Schemes
    • Add NGS MLST Report to Scheme
    • Merge MLST Schemes
    • Add Sequences to MLST Schemes
    • Map to Specified Reference (legacy)
      • How to run the Map to Specified Reference (legacy) workflow on a single sample
      • How to run the Map to Specified Reference (legacy) workflow on a batch of samples
    • Type among Multiple Species (legacy)
      • Preliminary steps to run the Type Multiple Species workflow
      • How to run the Type among Multiple Species (legacy) workflow
      • Example of results obtained using the Type among Multiple Species (legacy) workflow
    • Type a Known Species (legacy)
      • Preliminary steps to run the Type a Known Species (legacy) workflow
      • How to run the Type a Known Species (legacy) workflow
      • Example of results obtained using the Type a Known Species (legacy) workflow
  • 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

Introduction

Welcome to CLC Microbial Genomics Module 21.1 - a software package supporting your daily bioinformatics work.

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Subsections

• The concept of CLC Microbial Genomics Module
• Contact information

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